SWISS-PROT RELEASE 38.0 RELEASE NOTES
1. INTRODUCTION
Release 38.0 of SWISS-PROT contains 80'000 sequence entries, comprising
29'085'265 amino acids abstracted from 64'965 references. This represents
an increase of 3% over release 37. The growth of the data bank is
summarized below.
Release Date Number of Number of amino
entries acids
2.0 09/86 3939 900 163
3.0 11/86 4160 969 641
4.0 04/87 4387 1 036 010
5.0 09/87 5205 1 327 683
6.0 01/88 6102 1 653 982
7.0 04/88 6821 1 885 771
8.0 08/88 7724 2 224 465
9.0 11/88 8702 2 498 140
10.0 03/89 10008 2 952 613
11.0 07/89 10856 3 265 966
12.0 10/89 12305 3 797 482
13.0 01/90 13837 4 347 336
14.0 04/90 15409 4 914 264
15.0 08/90 16941 5 486 399
16.0 11/90 18364 5 986 949
17.0 02/91 20024 6 524 504
18.0 05/91 20772 6 792 034
19.0 08/91 21795 7 173 785
20.0 11/91 22654 7 500 130
21.0 03/92 23742 7 866 596
22.0 05/92 25044 8 375 696
23.0 08/92 26706 9 011 391
24.0 12/92 28154 9 545 427
25.0 04/93 29955 10 214 020
26.0 07/93 31808 10 875 091
27.0 10/93 33329 11 484 420
28.0 02/94 36000 12 496 420
29.0 06/94 38303 13 464 008
30.0 10/94 40292 14 147 368
31.0 02/95 43470 15 335 248
32.0 11/95 49340 17 385 503
33.0 02/96 52205 18 531 384
34.0 10/96 59021 21 210 389
35.0 11/97 69113 25 083 768
36.0 07/98 74019 26 840 295
37.0 12/98 77977 28 268 293
38.0 07/99 80000 29 085 965
2. DESCRIPTION OF THE CHANGES MADE TO SWISS-PROT SINCE RELEASE 37
2.1 Sequences and annotations
2'106 sequences have been added since release 37, the sequence data of 400
existing entries has been updated and the annotations of 12'576 entries
have been revised.
2.2 What's happening with the model organisms
We have selected a number of organisms that are the target of genome
sequencing and/or mapping projects and for which we intend to:
o Be as complete as possible. All sequences available at a given time
should be immediately included in SWISS-PROT. This also includes
sequence corrections and updates;
o Provide a higher level of annotation;
o Provide cross-references to specialized database(s) that contain,
among other data, some genetic information about the genes that code
for these proteins;
o Provide specific indices or documents.
Here is the current status of the model organisms in SWISS-PROT:
Organism Database Index file Number of
cross-referenced sequences
-------------- ---------------- -------------- ---------
A.thaliana None yet In preparation 821
B.subtilis SubtiList SUBTILIS.TXT 2069
C.albicans None yet CALBICAN.TXT 221
C.elegans Wormpep CELEGANS.TXT 2202
D.discoideum DictyDB DICTY.TXT 292
D.melanogaster FlyBase FLY.TXT 1088
E.coli EcoGene ECOLI.TXT 4516
H.influenzae HiDB (TIGR) HAEINFLU.TXT 1698
H.sapiens MIM MIMTOSP.TXT 5406
H.pylori HpDB (TIGR) HPYLORI.TXT 382
M.genitalium MgDB (TIGR) MGENITAL.TXT 469
M.musculus MGD MGDTOSP.TXT 3549
M.jannaschii MjDB (TIGR) MJANNASC.TXT 1312
M.tuberculosis None yet None yet 928
S.cerevisiae SGD YEAST.TXT 4811
S.typhimurium StyGene SALTY.TXT 727
S.pombe None yet POMBE.TXT 1438
S.solfataricus None yet None yet 86
-------------- ---------------- -------------- ---------
Collectively the entries from the above model organisms represent 38.5% of
all SWISS-PROT entries.
We plan to finish as quickly as possible the annotation of the Escherichia
coli, Haemophilus influenzae, Methanococcus jannaschii and yeast
(S.cerevisiae) sequence entries which are not yet part of SWISS-PROT.
Please also see the description of the Human Proteomics Initiative in
section 10 of these release notes.
2.3 First steps in the conversion of SWISS-PROT to mixed-case characters
We are gradually converting SWISS-PROT entries from all UPPER CASE to MiXeD
CaSe. The line-types that have been converted between release 37 and 38
are: DT (DaTe), OS (Organism Species), OC (Organism Classification), OG
(OrGanelle), RL (Reference Location) and KW (KeyWord). The RT (Reference
Title) lines were already introduced in mixed-case at release 37. As
described in section 3.1, the process of converting all of SWISS-PROT to
mixed case is continuing.
2.4 Small change in the format of RL lines for submissions to the DNA
databases
Along with the conversion of the RL to mixed-case (see 2.3) we have also
made a small change to the format of RL lines for submissions to the DNA
databases. What used to be:
RL SUBMITTED (MMM-YEAR) TO EMBL/GENBANK/DDBJ DATA BANKS.
is now:
RL Submitted (MMM-YEAR) to the EMBL/GenBank/DDBJ databases.
This change was made to follow more closely the format used by the EMBL
nucleotide sequence database.
2.5 Introduction of a new CC line-type topic: MISCELLANEOUS
We have introduced in this release a new 'topic' for the comments (CC) line
type: MISCELLANEOUS. This topic is used for all comments which do not
belong to any other already defined topic. This means that starting with
the current release all comments are now assigned to a topic. Example, what
was previously:
CC -!- BINDS TO BACITRACIN.
is now:
CC -!- MISCELLANEOUS: BINDS TO BACITRACIN.
2.6 Cleaning up of the SIMILARITY comment line (CC) topic
We are continuing a major overhaul of the SIMILARITY topic. We would like
the majority of the information stored in this topic to be usable by
computer programs (while being human-readable). We are therefore
standardizing the format of this topic using two different subformats. One
to describe to which family a protein belongs:
CC -!- SIMILARITY: BELONGS TO THE <Name1> FAMILY [OF <Name2>].
CC [<Name3> SUBFAMILY.]
Examples:
CC -!- SIMILARITY: BELONGS TO THE 14-3-3 FAMILY.
CC -!- SIMILARITY: BELONGS TO THE 6-PHOSPHOGLUCONATE DEHYDROGENASE
CC FAMILY.
CC -!- SIMILARITY: BELONGS TO THE AAA FAMILY OF ATPASES.
CC -!- SIMILARITY: BELONGS TO THE IRON/ASCORBATE-DEPENDENT FAMILY OF
CC OXIDOREDUCTASES.
CC -!- SIMILARITY: BELONGS TO THE ANTP FAMILY OF HOMEOBOX PROTEINS.
CC "DEFORMED" SUBFAMILY.
CC -!- SIMILARITY: BELONGS TO THE KINESIN-LIKE PROTEIN FAMILY.
CC KINESIN SUBFAMILY.
And one to describe which domains are found in a given protein:
CC -!- SIMILARITY: CONTAINS n <Name> [DOMAIN|REPEAT][S].
Examples:
CC -!- SIMILARITY: CONTAINS 1 FHA DOMAIN.
CC -!- SIMILARITY: CONTAINS 45 EGF-LIKE DOMAINS.
CC -!- SIMILARITY: CONTAINS 2 SH3 DOMAINS.
CC -!- SIMILARITY: CONTAINS 2 SUSHI (SCR) REPEATS.
We have already updated many entries in this and the previous releases and
plan to complete this change for the next release.
2.7 Changes concerning cross-references (DR line)
We have added cross-references from SWISS-PROT to the Zebrafish Information
Network (ZFIN) database available at http://zfish.uoregon.edu/ZFIN/ (see:
Westerfield M., Doerry E., Kirkpatrick A.E. and Douglas S.A.; Meth. Cell
Biol. 60:339-355(1999)). These cross-references are present in the DR
lines:
Data bank identifier: ZFIN
Primary identifier : The ZFIN identifiers for a given gene.
Secondary identifier: The gene designation
Example : DR ZFIN; ZDB-GENE-980526-290; hoxa1.
We have started to add cross-references from SWISS-PROT to the CarbBank
Complex Carbohydrate Structure Database (CCSD)
(http://128.192.9.29/carbbank/). These cross-references are present in the
DR lines:
Data bank identifier: CARBBANK
Primary identifier : The CarbBank identifier for a given carbohydrate
structure.
Secondary identifier: A dash (-).
Example : DR CARBBANK; CCSD:27494; -.
In this release, we have also updated all the DR lines pointing to the MIM
and Pfam databases.
2.8 Switching from pID to protein_ID in cross-references to the DNA
sequence databases
The DNA sequence databases (EMBL/GenBank/DDBJ) recently changed their
referencing system for CDS (CoDing Sequence). They used to associate every
CDS in the database with what was called a pID. The pID was a string of
variable length composed of a letter (D, E or G) followed by a number
(example: E345673). Whenever the protein sequence coded by a CDS would
change due to a sequence or annotation revision, a new pID was attributed
to that CDS. This system made it difficult to track down changes. pID have
therefore been replaced by what is now called protein_ID' (protein sequence
IDentifier). The protein_ID consists of a stable ID portion (8 characters:
3 letters followed by 5 numbers) plus a version number after a decimal
point (example: AAA03208.1). The version number only changes when the
protein sequence coded by the CDS changes, while the stable part remains
unchanged.
In release 38, we have converted the cross-references to EMBL/GenBank/DDBJ
to use the protein_ID instead of the pID as the secondary identifier in
these DR lines. Example, what was previously:
DR EMBL; Z75208; E1165324; -.
is now:
DR EMBL; Z75208; CAA99603.1; -.
For a number of technical reasons, there are still 732 pID referenced in
release 38, they will gradually be replaced by the corresponding protein_ID
for release 39.
2.9 Introduction of a unique identifier in the VARIANT feature description
of human sequence entries
We have introduced in release 38 a unique identifier for all VARIANT
feature keys in human sequence entries. This change is the first step
toward providing a unique identifier to all SWISS-PROT features. Human
sequence variants were chosen as a prototype for this improvement. It is
now possible to directly link specific sequence variants to the relevant
entries in disease mutation databases as well as to provide these databases
with a method to implement reciprocal links.
The unique identifier is of the form of /FTId=VAR_nnnnnn and is added as
the last part of the description field of 'VARIANT' feature keys. Example,
what was previously:
FT VARIANT 6 6 E -> V (IN S; SICKLE CELL ANEMIA).
FT VARIANT 11 11 V -> D (IN WINDSOR; O2 AFFINITY UP;
FT UNSTABLE).
is now:
FT VARIANT 6 6 E -> V (IN S; SICKLE CELL ANEMIA).
FT /FTId=VAR_002863.
FT VARIANT 11 11 V -> D (IN WINDSOR; O2 AFFINITY UP;
FT UNSTABLE).
FT /FTId=VAR_002873.
3. FORTHCOMING CHANGES
3.1 Continuation of the conversion of SWISS-PROT to mixed-case characters
We will continue to convert SWISS-PROT entries from all UPPER CASE to MiXeD
CaSe. In release 39 we are planning to convert the RA (Reference Author)
and RC (Reference Comment) line types. We will also convert the gene
designations in the DR (Database cross-Reference) lines for MGD, EcoGene,
StyGene, SubtiList and DictyDb to mixed case.
Further lines will be converted in release 40.
Here is an example of what a SWISS-PROT entry will look like in release 39:
ID HXC4_MOUSE STANDARD; PRT; 264 AA.
AC Q08624;
DT 01-OCT-1994 (Rel. 30, Created)
DT 01-OCT-1994 (Rel. 30, Last sequence update)
DT 15-DEC-1999 (Rel. 39, Last annotation update)
DE HOMEOBOX PROTEIN HOX-C4 (HOX-3.5).
GN HOXC4 OR HOXC-4 OR HOX-3.5.
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
OC Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Mus.
RN [1]
RP SEQUENCE FROM N.A.
RC STRAIN=Balb/C; TISSUE=Liver;
RX MEDLINE; 93288004.
RA Goto J., Miyabayashi T., Wakamatsu Y., Takahashi N., Muramatsu M.;
RT "Organization and expression of mouse Hox3 cluster genes.";
RL Mol. Gen. Genet. 239:41-48(1993).
RN [2]
RP SEQUENCE FROM N.A.
RC TISSUE=Embryo;
RX MEDLINE; 93161956.
RA Geada A.M.C., Gaunt S.J., Azzawi M., Shimeld S.M., Pearce J.,
RA Sharpe P.T.;
RT "Sequence and embryonic expression of the murine Hox-3.5 gene.";
RL Development 116:497-506(1992).
RN [3]
RP SEQUENCE OF 177-201 FROM N.A.
RC STRAIN=C57BL/6; TISSUE=Spleen;
RX MEDLINE; 92073357.
RA Murtha M.T., Leckman J.F., Ruddle F.H.;
RT "Detection of homeobox genes in development and evolution.";
RL Proc. Natl. Acad. Sci. U.S.A. 88:10711-10715(1991).
CC -!- FUNCTION: SEQUENCE-SPECIFIC TRANSCRIPTION FACTOR WHICH IS PART OF
CC A DEVELOPMENTAL REGULATORY SYSTEM THAT PROVIDES CELLS WITH
CC SPECIFIC POSITIONAL IDENTITIES ON THE ANTERIOR-POSTERIOR AXIS.
CC -!- SUBCELLULAR LOCATION: NUCLEAR.
CC -!- SIMILARITY: BELONGS TO THE ANTP FAMILY OF HOMEOBOX PROTEINS.
CC "DEFORMED" SUBFAMILY.
DR EMBL; D11328; BAA01947.1; -.
DR EMBL; S62287; AAB27153.1; -.
DR EMBL; X69019; CAA48784.1; -.
DR EMBL; M81660; AAA63313.1; -.
DR PIR; S35219; S35219.
DR HSSP; P02833; 1SAN.
DR MGD; MGI:96195; Hoxc4.
DR PFAM; PF00046; homeobox; 1.
DR PROSITE; PS00027; HOMEOBOX_1; 1.
DR PROSITE; PS00032; ANTENNAPEDIA; 1.
DR PROSITE; PS50071; HOMEOBOX_2; 1.
KW Homeobox; DNA-binding; Developmental protein; Nuclear protein;
KW Transcription regulation.
FT DOMAIN 54 60 POLY-PRO.
FT DOMAIN 135 140 ANTP-TYPE HEXAPEPTIDE (BY SIMILARITY).
FT DNA_BIND 156 215 HOMEOBOX (BY SIMILARITY).
FT DOMAIN 183 186 POLY-ARG.
FT CONFLICT 80 80 A -> G (IN REF. 2).
FT CONFLICT 96 96 P -> S (IN REF. 2).
SQ SEQUENCE 264 AA; 29865 MW; 611C069F CRC32;
MIMSSYLMDS NYIDPKFPPC EEYSQNSYIP EHSPEYYGRT RESGFQHHHQ ELYPPPPPRP
SYPERQYSCT SLQGPGNSRA HGPAQAGHHH PEKSQPLCEP APLSGTSASP SPAPPACSQP
APDHPSSAAS KQPIVYPWMK KIHVSTVNPN YNGGEPKRSR TAYTRQQVLE LEKEFHYNRY
LTRRRRIEIA HSLCLSERQI KIWFQNRRMK WKKDHRLPNT KVRSAPPAGA APSTLSAATP
GTSEDHSQSA TPPEQQRAED ITRL
//
3.2 Extension of the accession number system
With the creation of the TrEMBL database (see section 6) and the rapid
increase in the amount of sequence data, we are faced with a problem of
availability of accession numbers. Currently we use a system based on a
one-letter prefix followed by 5 digits. This system was also used by the
nucleotide sequence databases which had originally reserved for SWISS-PROT
the prefix letters O, 'P' and 'Q'. The nucleotide databases, having run out
of space (due mainly to EST's), have been forced to start using a new
format based on a two-letter prefix followed by 6 digits.
We have now used up all possible numbers with O, 'P' and 'Q'. As we believe
that changing the format of the accession numbers to that used now by the
nucleotide database would create havoc on the numerous software packages
using SWISS-PROT, we have decided to keep a system of accession numbers
based on a six-character code, but with the following format extension:
1 2 3 4 5 6
[O,P,Q] [0-9] [A-Z, 0-9] [A-Z, 0-9] [A-Z, 0-9] [0-9]
What the above means is that we will keep a six-character code, but that in
positions 3, 4 and 5 of this code any combination of letters and numbers
can be present. This format allows a total of 14 million accession numbers
(up from 300'000 with the current system).
We only allow numbers in positions 2 and 6 so that the SWISS-PROT accession
numbers can not be mistaken with gene names, acronyms, other type of
accession numbers or any type of words!
Examples: P0A3S2, Q2ASD4, O13YX2, P9B123
3.3 Introduction of a new FT key: SE_CYS
Selenocysteine is the 21st natural amino acid. It is now known to occur in
several dozen proteins. Its mRNA codon is UGA, which usually serves as a
stop codon, but with a specific downstream sequence forming a loop and a
specific translational elongation factor. It is recognized as the site of
selenocysteine incorporation into proteins.
Very recently the joint nomenclature committee of the IUPAC/IUBMB (see
http:// www.chem.qmw.ac.uk/iupac/jcbn/) officially recommended
(http://www.chem.qmw.ac.uk/iubmb/newsletter/1999/item3.html) a three-letter
and a one-letter symbol for selenocysteine, namely Sec and U.
We recognize that introducing a new one-letter code in the sequence records
would disrupt most, if not all, sequence analysis software. We therefore
decided to change, in SWISS-PROT, the rules used to annotate the presence
of selenocysteine residues in sequence entries in the manner described
below.
Currently selenocysteines are stored, in the sequence records, using the
one-letter symbol C for cysteine and are indicated in the feature table
(FT) by a line of the type:
FT BINDING x x SELENIUM.
The one-letter code will not be changed (for the reason explained above),
but we will introduce a specific feature key (SE_CYS) to indicate the
presence of a selenocysteine at a given sequence position. The above
example will therefore be changed to:
FT SE_CYS x x
We also want to remind users that the keyword Selenocysteine is and will
continue to be used to tag sequence entries that contain at least one such
residue.
3.4 Introduction of a new CC line-type topic: PHARMACEUTICAL
We will introduce in the next release a new 'topic' for the comments (CC)
line type: PHARMACEUTICAL. This topic will describe the use of a specific
protein as a pharmaceutical drug. The information provided by such a topic
will include the brand name(s) under which a protein is available, the
name(s) of the compani(es) that produce it as well as a short description
of the therapeutic usage of the protein.
Examples:
CC -!- PHARMACEUTICAL: Available under the names Avonex (Biogen),
CC Betaseron (Berlex) and Rebif (Serono). Used in the treatment
CC of multiple sclerosis (MS). Betaseron is a slightly modified
CC form of IFNB1 with two residue substitutions.
CC -!- PHARMACEUTICAL: Available under the name Proleukin (Chiron).
CC Used in patients with renal cell carcinoma or metastatic
CC melanoma.
It should be noted that any entries containing such a comment field will
also be tagged with the keyword Pharmaceutical.
3.5 Multiple AC lines
Starting with release 39, there can be more than one AC (ACcession) line
per SWISS-PROT entry. Strictly speaking this is not a format change and the
users manual of SWISS-PROT always indicated that there could be more than
one AC line per entry. Until recently, a single line was sufficient and the
majority of entries contained only a single accession number. But, in the
process of providing an optimally non-redundant database we are merging
information from TrEMBL entries into SWISS-PROT entries. When we merge a
TrEMBL entry to a SWISS-PROT one, we add to that SWISS-PROT entry the
accession number(s) of the TrEMBL entry. The repetition of such a process
sometimes produces an accession number list which can no longer fit in a
single AC line. Therefore there will now be some entries with two, three
(as shown below) or more AC lines.
AC P16070; P22511; Q04858; Q13419; Q13957; Q13958; Q13959; Q13960;
AC Q13961; Q13967; Q13968; Q13980; Q15861; Q16064; Q16065; Q16066;
AC Q16208; Q16522;
3.6 Change in the syntax of the SQ line
The SQ (SeQuence header) line marks the beginning of the sequence data and
gives a quick summary of its content. The format of the SQ line is
currently:
SQ SEQUENCE XXXX AA; XXXXXX MW; XXXXXXXX CRC32;
The last information item in the SQ line is a 32-bit CRC (Cyclic Redundancy
Check) value which is computed from the sequence. As the number of
available sequences is increasing rapidly, there are now a few cases where
two sequences can share the same CRC32 (but none, which also share the same
molecular weight MW or number of amino acids AA). To address this issue we
will, starting with the next release, replace the 32-bit CRC value by a 64-
bit CRC. The format of the SQ line will therefore be changed to:
SQ SEQUENCE XXXX AA; XXXXXX MW; XXXXXXXXXXXXXXXX CRC64;
Example:
SQ SEQUENCE 233 AA; 25630 MW; 146A1B48A1475C86 CRC64;
4. STATUS OF THE DOCUMENTATION FILES
SWISS-PROT is distributed with a large number of documentation files. Some
of these files have been available for a long time (the user manual,
release notes, the various indices for authors, citations, keywords, etc.),
but many have been created recently and we are continuously adding new
files. The following table lists all the documents that are currently
available.
USERMAN.TXT User manual
RELNOTES.TXT Release notes for current release (38)
OLDRLNOT.TXT Release notes for previous release (37)
SHORTDES.TXT Short description of entries in SWISS-PROT
JOURLIST.TXT List of abbreviations for journals cited
KEYWLIST.TXT List of keywords in use
SPECLIST.TXT List of organism identification codes
TISSLIST.TXT List of tissues [See 1]
EXPERTS.TXT List of on-line experts for PROSITE and SWISS-PROT
SUBMIT.TXT Submission of sequence data to SWISS-PROT
ACINDEX.TXT Accession number index
AUTINDEX.TXT Author index
CITINDEX.TXT Citation index
KEYINDEX.TXT Keyword index
SPEINDEX.TXT Species index
DELETEAC.TXT Deleted accession number index
7TMRLIST.TXT List of 7-transmembrane G-linked receptors entries
AATRNASY.TXT List of aminoacyl-tRNA synthetases
ALLERGEN.TXT Nomenclature and index of allergen sequences
ANNBIOCH.TXT SWISS-PROT annotation: how is biochemical information
assigned to sequence entries [See 2]
BLOODGRP.TXT List of blood group antigen proteins
CALBICAN.TXT Index of Candida albicans entries and their
corresponding gene designations
CDLIST.TXT CD nomenclature for surface proteins of human
leucocytes
CELEGANS.TXT Index of Caenorhabditis elegans entries and their
corresponding gene Wormpep cross-references
DICTY.TXT Index of Dictyostelium discoideum entries and
their corresponding gene designations and DictyDb
cross-references
EC2DTOSP.TXT Index of Escherichia coli Gene-protein database
entries referenced in SWISS-PROT
ECOLI.TXT Index of Escherichia coli K12 chromosomal entries
and their corresponding EcoGene cross-references
EMBLTOSP.TXT Index of EMBL Database entries referenced in
SWISS-PROT
EXTRADOM.TXT Nomenclature of extracellular domains
FLY.TXT Index of Drosophila entries and FlyBase cross-
references
GLYCOSID.TXT Classification of glycosyl hydrolase families and
index of glycosyl hydrolase entries
HAEINFLU.TXT Index of Haemophilus influenzae RD chromosomal
entries
HOXLIST.TXT Vertebrate homeotic Hox proteins: nomenclature and
index
HPYLORI.TXT Index of Helicobacter pylori strain 26695
chromosomal entries
HUMCHR16.TXT Index of protein sequence entries encoded on human
chromosome 16 [See 2]
HUMCHR17.TXT Index of protein sequence entries encoded on human
chromosome 17
HUMCHR18.TXT Index of protein sequence entries encoded on human
chromosome 18
HUMCHR19.TXT Index of protein sequence entries encoded on human
chromosome 19
HUMCHR20.TXT Index of protein sequence entries encoded on human
chromosome 20
HUMCHR21.TXT Index of protein sequence entries encoded on human
chromosome 21
HUMCHR22.TXT Index of protein sequence entries encoded on human
chromosome 22
HUMCHRX.TXT Index of protein sequence entries encoded on human
chromosome X
HUMCHRY.TXT Index of protein sequence entries encoded on human
chromosome Y
HUMPVAR.TXT Index of human proteins with sequence variants
INITFACT.TXT List and index of translation initiation factors
MIMTOSP.TXT Index of MIM entries referenced in SWISS-PROT
METALLO.TXT Classification of metallothioneins and index of
entries in SWISS-PROT
MGDTOSP.TXT Index of MGD entries referenced in SWISS-PROT
MGENITAL.TXT Index of Mycoplasma genitalium chromosomal entries
MJANNASC.TXT Index of Methanococcus jannaschii entries
NGR234.TXT Table of putative genes in Rhizobium plasmid
pNGR234a
NOMLIST.TXT List of nomenclature related references for
proteins
PCC6803.TXT Index of Synechocystis strain PCC 6803 entries
PDBTOSP.TXT Index of X-ray crystallography Protein Data Bank
(PDB) entries referenced in SWISS-PROT
PEPTIDAS.TXT Classification of peptidase families and index of
peptidase entries
PLASTID.TXT List of chloroplast and cyanelle encoded proteins
POMBE.TXT Index of Schizosaccharomyces pombe entries in
SWISS-PROT and their corresponding gene
designations
RESTRIC.TXT List of restriction enzyme and methylase entries
RIBOSOMP.TXT Index of ribosomal proteins classified by families
on the basis of sequence similarities
SALTY.TXT Index of Salmonella typhimurium LT2 chromosomal
entries and their corresponding StyGene cross-
references
SUBTILIS.TXT Index of Bacillus subtilis 168 chromosomal entries
and their corresponding SubtiList cross-references
UPFLIST.TXT UPF (Uncharacterized Protein Families) list and
index of members
YEAST.TXT Index of Saccharomyces cerevisiae entries and
their corresponding gene designations
YEAST1.TXT Yeast Chromosome I entries
YEAST2.TXT Yeast Chromosome II entries
YEAST3.TXT Yeast Chromosome III entries
YEAST5.TXT Yeast Chromosome V entries
YEAST6.TXT Yeast Chromosome VI entries
YEAST7.TXT Yeast Chromosome VII entries
YEAST8.TXT Yeast Chromosome VIII entries
YEAST9.TXT Yeast Chromosome IX entries
YEAST10.TXT Yeast Chromosome X entries
YEAST11.TXT Yeast Chromosome XI entries
YEAST13.TXT Yeast Chromosome XIII entries
YEAST14.TXT Yeast Chromosome XIV entries
1. The tissue list (tisslist.txt) has been converted to mixed-case
characters;
2. The annbioch.txt and humchr16.txt files are new documents introduced
in this release.
We have continued to include in some SWISS-PROT documentation files the
references of Web sites relevant to the subject under consideration. There
are now 42 documents that include such links.
5. THE EXPASY WORLD-WIDE WEB SERVER
5.1 Background information
The most efficient and user-friendly way to browse interactively in SWISS-
PROT, PROSITE, ENZYME, SWISS-2DPAGE and other databases is to use the
World-Wide Web (WWW) molecular biology server ExPASy. The ExPASy server was
made available to the public in September 1993 and is reachable at the
following address:
http://www.expasy.ch/
The ExPASy WWW server allows access, using the user-friendly hypertext
model, to the SWISS-PROT, PROSITE, ENZYME, SWISS-2DPAGE, SWISS-3DIMAGE and
CD40Lbase databases. And, through any SWISS-PROT protein sequence entry, to
other databases such as EMBL, Eco2DBASE, EcoCyc, EcoGene, FlyBase, GCRDb,
MaizeDB, Mendel, OMIM, PDB, HSSP, Pfam, ProDom, REBASE, SGD,
SubtiList/NRSub, TRANSFAC, YPD, ZFIN and Medline. ExPASy also offers many
tools for the analysis of protein sequences and 2D gels.
5.2 Swiss-Shop
We provide, on ExPASy, a service called Swiss-Shop
(http://www.expasy.ch/swiss-shop/). Swiss-Shop is an automated sequence
alerting system which allows users to obtain, by email, new sequence
entries relevant to their field(s) of interest. Various criteria can be
combined:
- By entering one or more words that should be present in the
description line;
- By entering one or more species name(s) or taxonomic division(s);
- By entering one or more keywords;
- By entering one or more author names;
- By entering the accession number (or entry name) of a PROSITE pattern
or a user-defined sequence pattern;
- By entering the accession number (or entry name) of an existing SWISS-
PROT entry or by entering a private sequence.
Every week, the new sequences entered in SWISS-PROT are automatically
compared with all the criteria that have been defined by the users. If a
sequence corresponds to the selection criteria defined by a user, that
sequence is sent by electronic mail.
5.3 What is new on ExPASy
ExPASy is constantly modified and improved. If you wish to be informed on
the changes made to the server you can either:
- Read the document History of changes, improvements and new features
which is available at the address: http://www.expasy.ch/history.html
- Subscribe to Swiss-Flash, a service that reports news of databases,
software and service developments. By subscribing to this service, you
will automatically get Swiss-Flash bulletins by electronic mail. To
subscribe use the address: http://www.expasy.ch/ swiss-flash/
Among all the improvements and the new features introduced during the last
three months, here are those that we believe are specifically useful to
SWISS-PROT users:
1. We have switched our default view of SWISS-PROT entry to that provided
by the NiceProt tool. NiceProt offers a user-friendly tabular view of
SWISS-PROT entries. Access to the original SWISS-PROT format is
maintained and is directly available from the NiceProt view. Tools with
similar functionalities have been developed to display the ENZYME and
PROSITE databases (see section 8.1 and 8.2).
2. We have revised the ExPASy file and directory structure, in order to
have the vast amount of data that has accumulated on the server since
September 1993 available in a more structured manner, and to facilitate
replication on our mirror sites. This has caused certain changes in html
links, and you should update your bookmarks and links accordingly. If in
doubt, please refer to the document 'How to create html links to ExPASy'
(http://www.expasy.ch/expasy_urls.html). At the same time we wish to
reiterate our announcement of the ExPASy mirror sites in Australia
(http://expasy.proteome.org.au/) and Taiwan (http://expasy.nhri.org.tw/).
For your own convenience, please use the mirror site closest to you.
Please also make sure to update all bookmarks or links that use the old
domain expasy.hcuge.ch, which was replaced by www.expasy.ch in March
1997! The 'expasy.hcuge.ch' address might be disabled in the near future.
3. WWW links have been implemented between SWISS-PROT and CarbBank,
EcoGene and ZFIN.
6. TREMBL - A SUPPLEMENT TO SWISS-PROT
The ongoing genome sequencing and mapping projects have dramatically
increased the number of protein sequences to be incorporated into SWISS-
PROT. Since we do not want to dilute the quality standards of SWISS-PROT by
incorporating sequences into the database without proper sequence analysis
and annotation, we cannot speed up the incorporation of new incoming data
indefinitely. But as we also want to make the sequences available as fast
as possible, we have introduced with SWISS-PROT a computer annotated
supplement. This supplement consists of entries in SWISS-PROT-like format
derived from the translation of all coding sequences (CDS) in the EMBL
nucleotide sequence database, except those already included in SWISS-PROT.
This supplement is named TrEMBL (Translation from EMBL). It can be
considered as a preliminary section of SWISS-PROT. This SWISS-PROT release
is supplemented by TrEMBL release 11. TrEMBL is split in two main sections;
SP-TrEMBL and REM-TrEMBL:
SP-TrEMBL (SWISS-PROT TrEMBL) contains the entries (199'794 in release 11)
which should be incorporated into SWISS-PROT. SWISS-PROT accession numbers
have been assigned for all SP-TrEMBL entries.
REM-TrEMBL (REMaining TrEMBL) contains the entries (45'967 in release 11)
that we do not want to include in SWISS-PROT for a variety of reasons
(synthetic sequences, pseudogenes, translations of incorrect open reading
frames, fragments with less than eight amino acids, patent-derived
sequences, immunoglobulins and T-cell receptors, etc.)
TrEMBL is available by FTP from the EBI and ExPASy servers in the directory
databases/trembl'. It can be queried on WWW by the EBI and ExPASy SRS
servers. It is also searchable on the FASTA, BIC_SW and BLAST servers of
the EBI.
7. FTP ACCESS TO SWISS-PROT AND TREMBL
7.1 Generalities
SWISS-PROT is available for download on the following anonymous FTP
servers:
Organization Swiss Institute of Bioinformatics (SIB)
Address ftp.expasy.ch
Directory /databases/swiss-prot/
Organization European Bioinformatics Institute (EBI)
Address ftp.ebi.ac.uk
Directory /pub/databases/swissprot/
7.2 Weekly updates of SWISS-PROT
Weekly updates of SWISS-PROT are available by anonymous FTP. Three files
are generated at each update:
new_seq.dat Contains all the new entries since the last full release;
upd_seq.dat Contains the entries for which the sequence data has been
updated since the last release;
upd_ann.dat Contains the entries for which one or more annotation fields
have been updated since the last release.
Important notes
o Although we try to follow a regular schedule, we do not promise to update
these files every week. In most cases two weeks may elapse between two
updates.
o Instead of using the above files, you can, every week, download an
updated copy of the SWISS-PROT database. This file is available in the
directory containing the non-redundant database (see next section).
7.3 Non-redundant database
More than a year ago, we started to distribute on the ExPASy and EBI FTP
servers, files that make up a non-redundant (see further) and complete
protein sequence database consisting of three components:
1) SWISS-PROT
2) TrEMBL
3) New entries to be later integrated into TrEMBL (hereafter known as
TrEMBL_New)
Every week three files are completely rebuilt. These files are named:
sprot.dat.Z, trembl.dat.Z and trembl_new.dat.Z. As indicated by their .Z
extension these are Unix compress format files which, when decompressed,
will produce ASCII files in SWISS-PROT format.
Three other files are also available (sprot.fas.Z, trembl.fas.Z and
trembl_new.fas.Z) which are compressed fasta format sequence files useful
for building the databases used by FASTA, BLAST and other sequence
similarity search programs. Please do not use these files for any other
purpose, as you will lose all annotations by using this very primitive
format.
The files for the non-redundant database are stored in the directory
/databases/sp_tr_nrdb on the ExPASy FTP server (ftp.expasy.ch) and in the
directory /pub/databases/sp_tr_nrdb on the EBI FTP server (ftp.ebi.ac.uk).
Additional notes
o The SWISS-PROT file continuously grows as new annotated sequences are
added.
o The TrEMBL file decreases in size as sequences are moved out of that
section after being annotated and moved into SWISS-PROT. Four times a
year a new release of TrEMBL is built at EBI, at this point the TrEMBL
file increases in size as it then includes all of the new data (see next
section) that has accumulated since the last release.
o The TrEMBL_New file starts as a very small file and grows in size until a
new release of TrEMBL is available.
o SWISS-PROT and TrEMBL share the same system of accession numbers.
Therefore you will not find any primary accession number duplicated
between the two sections. A TrEMBL entry (and its associated accession
number(s)) can either move to SWISS-PROT as new entry or be merged with
an existing SWISS-PROT entry. In the latter case, the accession number(s)
of that TrEMBL entry are added to that of the SWISS-PROT entry.
o TrEMBL_New does not have real accession numbers. However it was necessary
to have an AC line so as to be able to use it with different software
products. This AC line contains a temporary identifier which consists of
the protein_ID (protein sequence identifier) of the coding sequence in
the parent nucleotide sequence.
o TrEMBL_New is quite messy! You will of course find new sequence entries
but you will also encounter sequences that are going to be used to update
existing TrEMBL or SWISS-PROT entries. None of the "cleaning" steps that
are applied to produce a TrEMBL release are run on TrEMBL_New nor are any
of the computer-annotation software tools that are used to enhance the
information content of TrEMBL. TrEMBL_New is provided only so that users
can be sure not to miss any important new sequences when they run
similarity searches.
o While these three files allow you to build what we call a non-redundant
database, it must be noted that this is not completely a true statement.
Without going into a long explanation we can say that this is currently
the best attempt in providing a complete selection of protein sequence
entries while trying to eliminate redundancies. Also SWISS-PROT is
completely (well 99.994% !) non-redundant, TrEMBL is far from being non-
redundant and the addition of SWISS-PROT + TrEMBL is even less.
o To describe to your users the version of the non-redundant database that
you are providing them with, you should use a statement of the form:
SWISS-PROT release 38 and updates until <current_date>;
TrEMBL release 11 minus data integrated into SWISS-PROT as of
<current_date>;
New preliminary TrEMBL entries created since release 11 of TrEMBL
8. ENZYME AND PROSITE
8.1 The ENZYME nomenclature database
Release 25.0 of the ENZYME nomenclature database is distributed with
release 38 of SWISS-PROT. ENZYME release 25.0 contains information relative
to 3704 enzymes. In this release, we have added a significant number of
synonyms (AN lines) to a number of entries.
The WWW version of ENZYME on ExPASy now provides a more user-friendly
tabular view of enzyme entries through a new tool called NiceZyme. NiceZyme
also provides direct links, through Medline, to literature references
relevant to a specific enzyme. You can use this tool to link to any ENZYME
entry by using the following type of URL: http://www.expasy.ch/cgi-
bin/nicezyme.pl?a.b.c.d (where a.b.c.d is any valid enzyme EC number;
example: 1.2.1.1).
Please also note that the URL of the top page of ENZYME has moved to:
http://www.expasy.ch/enzyme/
8.2 The PROSITE database
Release 16.0 of the PROSITE database is distributed with release 38 of
SWISS-PROT. This release of PROSITE contains 1034 documentation entries
that describe 1'374 different patterns, rules and profiles/matrices. Since
release 15.0, 20 entries have been added and 180 entries have been updated.
The WWW version of PROSITE on ExPASy now provides a more user-friendly
tabular view of enzyme entries through a new tool called NiceSite. You can
use this tool to link to any PROSITE entry by using the following types of
URL: http://www.expasy.ch/cgi-bin/nicesite.pl?PSxxxxx (where PSxxxxx is any
valid PROSITE pattern or matrix entry) and http://www.expasy.ch/cgi-
bin/nicedoc.pl?PDOCxxxxx (where PDOCxxxxx is any valid PROSITE document
entry).
Please also note that the URL of the top page of PROSITE has moved to:
http://www.expasy.ch/prosite/
9. WE NEED YOUR HELP!
We welcome feedback from our users. We would especially appreciate that you
notify us if you find that sequences belonging to your field of expertise
are missing from the database. We also would like to be notified about
annotations to be updated, if, for example, the function of a protein has
been clarified or if new information about post-translational modifications
has become available. To facilitate this feedback we offer, on the ExPASy
WWW server, a form that allows the submission of updates and/or corrections
to SWISS-PROT:
http://www.expasy.ch/sprot/sp_update_form.html
It is also possible, from any entry in SWISS-PROT displayed by the ExPASy
server, to submit updates and/or corrections for that particular entry.
Finally, you can also send your comments by electronic mail to the address:
swiss-prot@expasy.ch
Note that since January 1999, all update requests are assigned a unique
identifier of the form UR-Xnnnn (example: UR-A0123). This identifier is
used internally by the SWISS-PROT staff at SIB and EBI to track down the
fate of requests and is also be used in email exchanges with the persons
having submitted a request.
10. JULY 1999 ANNOUNCEMENT: THE HUMAN PROTEOMICS INITIATIVE
In a few months the combined efforts of a number of sequencing centers and
companies will produce a first draft of the human genome sequence. Such an
endeavor is only a very preliminary step in the understanding of human
biological processes. The first pitfall to overcome is the detection of all
coding regions on the genomic sequence. Current algorithms, while being
very powerful, are not capable of detecting with certainty all exons, are
not well equipped to distinguish different splice variants and are unable
to detect small proteins (which are numerous and crucial to many biological
processes). Even when all potential coding regions have been predicted, the
user community will have at its disposition the sequence of from 80000 to
100000 naked proteins. We call these proteins naked because genomic
information does not allow the efficient prediction of all the post-
translational modifications (PTM) of which the majority of proteins are the
target. Proteins, once synthesized on the ribosomes, are subject to a
multitude of modification steps. The complexity due to all these
modifications is compounded by the high level of diversity that alternative
splicing can produce at the level of sequence. Thus the number of different
protein molecules expressed by the human genome is probably closer to a
million than to the hundred thousand generally considered by genome
scientists. Another factor of complexity to take into account is the amount
of polymorphism at the protein sequence level. While some of these
polymorphisms are linked to disease states, most are not, yet have in many
cases a direct or indirect effect on the activities of the proteins.
We therefore are initiating a major project to annotate all known human
sequences according to the quality standards of SWISS-PROT. This means
providing, for each known protein, a wealth of information that includes
the description of its function, its domain structure, subcellular
location, post-translational modifications, variants, similarities to other
proteins, etc. There are currently slightly more than 5400 annotated human
sequences in SWISS-PROT. These entries are associated with about 14500
literature references; 16000 experimental or predicted PTMs, 800 splice
variants and 8000 polymorphisms (most of which are linked with disease
states). We will use the current information as the ground basis for what
we call the Human Proteomics Initiative (HPI).
The HPI project contains a number of sub-components, which are briefly
described below:
ú Annotation of all known human proteins. In the course of the next nine
months (from July 1999 to end of March 2000) the human protein sequences
that are not yet in SWISS-PROT will be fully annotated. We will also
review and complete the annotation of the human sequences currently in
SWISS-PROT. At the end of this nine-month period we expect to be complete
and up-to-date and to hereafter keep up with the appearance of new data
relevant to human proteins.
ú Annotation of mammalian orthologs of human proteins. We will make sure
that for any human proteins, existing orthologs in other mammalian
species will also be annotated at a level equivalent to that of the
cognate human sequences.
ú Annotation of all known human polymorphisms at the protein sequence
level. As mentioned above, SWISS-PROT already holds information on a
sizeable amount of such polymorphisms, and it will significantly expand
its effort to store and annotate all small variations at the protein
level.
ú Annotation of all known post-translational modifications in human
proteins. During the next nine months a major effort will be made to
supplement the already quite comprehensive description of known post-
translational modifications in human proteins currently provided in
SWISS-PROT.
ú Tight links to structural information. SWISS-PROT is tightly linked to
the PDB/RCSB 3D-structure database and already includes many features
useful to structural biologists. These tight links will be further
expanded by providing homology-derived models for all human proteins for
which such an approach is scientifically relevant.
For all aspects of the HPI projects, we would appreciate the help and
collaboration of the scientific community. Information concerning the human
proteome is highly critical to a large section of the life science
community. We therefore appeal to the user community to fully participate
in this initiative by providing all the necessary information to help and
to speed up the comprehensive annotation of the human proteome.
The HPI project has two different time-related aspects: one of which is a
nine-month "marathon" to catch up with the current state of research, the
other one is a long-term commitment to keep such a project alive as long as
it is necessary. For a detailed description of the HPI project and its
current status please consult:
http://www.expasy.ch/sprot/hpi/
11. JULY 1998 ANNOUNCEMENT: NEW SWISS-PROT FUNDING SCHEME
It became obvious in the last years that the tremendous increase in data
flow has created a requirement for resources which cannot be addressed in
full by public funding. This is causing databases to fall behind the
research. We believe that the only solution to the resource shortfall is to
ask commercial users to participate by paying a license fee. No fee is or
will be charged to academic users, nor is any restriction be imposed on
their use or reuse of the data. Both SWISS-PROT and PROSITE are concerned
by these changes, while this is not the case of ENZYME.
A document fully describing what will be the impact of this change for
SWISS-PROT is available with the SWISS-PROT distribution files on FTP
(sp_info.txt). You can also access the document as well as other relevant
ones from:
http://www.expasy.ch/announce/
http://www.ebi.ac.uk/swissprot/Information/Announcement/announcement.html
If you do not have the time to read this document, the most important take-
home message is that these changes do not have any impact on the way SWISS-
PROT or PROSITE are accessed or redistributed. Academic users are not
affected by these changes. Industrial end-users are also not directly
affected as long as their employer pays the license fee. The same holds
true for bioinformatics companies. Academic software or database developers
as well as providers of database distribution services are only minimally
affected by these changes. We hope to be able to keep the spirit of SWISS-
PROT and PROSITE alive and at the same time ensure their long-term
financial survival. We sincerely hope and believe that in the next two
years the only change that will matter will be the increase in scope and
timeliness of the databases.
========================================================================
APPENDIX A: SOME STATISTICS
A.1 Amino acid composition
A.1.1 Composition in percent for the complete data bank
Ala (A) 7.58 Gln (Q) 3.97 Leu (L) 9.43 Ser (S) 7.13
Arg (R) 5.16 Glu (E) 6.36 Lys (K) 5.94 Thr (T) 5.67
Asn (N) 4.44 Gly (G) 6.84 Met (M) 2.37 Trp (W) 1.24
Asp (D) 5.27 His (H) 2.24 Phe (F) 4.10 Tyr (Y) 3.19
Cys (C) 1.66 Ile (I) 5.81 Pro (P) 4.92 Val (V) 6.58
Asx (B) 0.001 Glx (Z) 0.001 Xaa (X) 0.01
A.1.2 Classification of the amino acids by their frequency
Leu, Ala, Ser, Gly, Val, Glu, Lys, Ile, Thr, Asp, Arg, Pro, Asn, Phe,
Gln, Tyr, Met, His, Cys, Trp
A.2 Repartition of the sequences by their organism of origin
Total number of species represented in this release of SWISS-PROT: 6580
The first twenty species represent 37741 sequences: 47.2 % of the total
number of entries.
A.2.1 Table of the frequency of occurrence of species
Species represented 1x: 3122
2x: 1013
3x: 509
4x: 363
5x: 243
6x: 225
7x: 154
8x: 127
9x: 105
10x: 62
11- 20x: 304
21- 50x: 191
51-100x: 73
>100x: 89
A.2.2 Table of the most represented species
------ --------- --------------------------------------------
Number Frequency Species
------ --------- --------------------------------------------
1 5406 Homo sapiens (Human)
2 4811 Saccharomyces cerevisiae (Baker's yeast)
3 4516 Escherichia coli
4 3549 Mus musculus (Mouse)
5 2630 Rattus norvegicus (Rat)
6 2069 Bacillus subtilis
7 2002 Caenorhabditis elegans
8 1698 Haemophilus influenzae
9 1438 Schizosaccharomyces pombe (Fission yeast)
10 1313 Methanococcus jannaschii
11 1149 Bos taurus (Bovine)
12 1088 Drosophila melanogaster (Fruit fly)
13 928 Mycobacterium tuberculosis
14 894 Gallus gallus (Chicken)
15 821 Arabidopsis thaliana (Mouse-ear cress)
16 729 Xenopus laevis (African clawed frog)
17 727 Salmonella typhimurium
18 699 Synechocystis sp. (strain PCC 6803)
19 670 Sus scrofa (Pig)
20 604 Oryctolagus cuniculus (Rabbit)
21 490 Mycoplasma pneumoniae
22 469 Mycoplasma genitalium
23 446 Zea mays (Maize)
24 403 Rhizobium sp. (strain NGR234)
25 382 Helicobacter pylori (Campylobacter pylori)
26 368 Pseudomonas aeruginosa
27 337 Oryza sativa (Rice)
28 308 Canis familiaris (Dog)
29 296 Nicotiana tabacum (Common tobacco)
30 292 Dictyostelium discoideum (Slime mold)
31 277 Treponema pallidum
32 272 Bacteriophage T4
33 269 Ovis aries (Sheep)
269 Mycobacterium leprae
35 266 Borrelia burgdorferi (Lyme disease spirochete)
36 263 Pisum sativum (Garden pea)
37 255 Methanobacterium thermoautotrophicum
38 253 Vaccinia virus (strain Copenhagen)
39 239 Glycine max (Soybean)
40 228 Staphylococcus aureus
41 227 Neurospora crassa
42 226 Hordeum vulgare (Barley)
43 221 Candida albicans (Yeast)
44 219 Porphyra purpurea
45 216 Archaeoglobus fulgidus
46 211 Lycopersicon esculentum (Tomato)
47 209 Triticum aestivum (Wheat)
48 205 Solanum tuberosum (Potato)
49 204 Rhodobacter capsulatus (Rhodopseudomonas capsulata)
50 199 Klebsiella pneumoniae
51 196 Pseudomonas putida
52 193 Human cytomegalovirus (strain AD169)
53 192 Bacillus stearothermophilus
54 186 Vaccinia virus (strain WR)
55 172 Cavia porcellus (Guinea pig)
56 170 Agrobacterium tumefaciens
57 169 Spinacia oleracea (Spinach)
58 159 Chlamydomonas reinhardtii
59 158 Rhizobium meliloti
60 154 Autographa californica nuclear polyhedrosis virus
61 153 Emericella nidulans (Aspergillus nidulans)
62 152 Mesocricetus auratus (Golden hamster)
63 151 Marchantia polymorpha (Liverwort)
64 150 Streptomyces coelicolor
150 Equus caballus (Horse)
66 148 Guillardia theta (Cryptomonas phi)
67 147 Cyanophora paradoxa
68 146 Variola virus
69 142 Lactococcus lactis (subsp. lactis) (Streptococcus lactis)
70 139 Odontella sinensis
71 134 Orgyia pseudotsugata multicapsid polyhedrosis virus
72 133 Kluyveromyces lactis (Yeast)
73 128 Brachydanio rerio (Zebrafish) (Zebra danio)
74 127 Trypanosoma brucei brucei
127 Synechococcus sp. (strain PCC 7942)
76 126 Thermus aquaticus (subsp. thermophilus)
77 120 Alcaligenes eutrophus
118 Anabaena sp. (strain PCC 7120)
79 116 Bombyx mori (Silk moth)
80 115 Bradyrhizobium japonicum
81 113 Yersinia enterocolitica
82 112 Oncorhynchus mykiss (Rainbow trout) (Salmo gairdneri)
83 111 Aquifex aeolicus
108 Streptococcus pneumoniae
85 107 Brassica napus (Rape)
86 104 Neisseria gonorrhoeae
87 103 Macaca mulatta (Rhesus macaque)
103 Felis silvestris catus (Cat)
89 102 Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
A.3 Repartition of the sequences by size
From To Number From To Number
1- 50 3213 1001-1100 722
51- 100 6704 1101-1200 553
101- 150 9719 1201-1300 377
151- 200 7640 1301-1400 251
201- 250 7202 1401-1500 210
251- 300 6703 1501-1600 133
301- 350 6294 1601-1700 117
351- 400 6438 1701-1800 89
401- 450 4831 1801-1900 94
451- 500 4566 1901-2000 65
501- 550 3444 2001-2100 37
551- 600 2308 2101-2200 80
601- 650 1801 2201-2300 75
651- 700 1326 2301-2400 40
701- 750 1159 2401-2500 42
751- 800 956 >2500 232
801- 850 762
851- 900 798
901- 950 552
951-1000 467
A.4 Longest sequences
The longest sequences (>=4000 residues) are listed here:
BACA_BACLI 5255
HTS1_COCCA 5217
MUC2_HUMAN 5179
FAT_DROME 5147
RYNR_RABIT 5037
RYNR_PIG 5035
RYNR_HUMAN 5032
RYNC_RABIT 4969
LRP_CAEEL 4753
DYHC_DICDI 4725
PLEC_RAT 4687
LRP2_RAT 4660
LRP2_HUMAN 4655
DYHC_RAT 4644
DYHC_DROME 4639
DYHC_CAEEL 4568
DYHB_CHLRE 4568
APB_HUMAN 4563
APOA_HUMAN 4548
LRP1_HUMAN 4544
LRP1_CHICK 4543
DYHC_PARTE 4540
RRPA_CVMJH 4488
DYHG_CHLRE 4485
DYHC_ANTCR 4466
DYHC_TRIGR 4466
GRSB_BACBR 4451
PKSK_BACSU 4447
PKSL_BACSU 4427
PGBM_HUMAN 4393
YP73_CAEEL 4385
DYHC_NEUCR 4367
DYHC_FUSSO 4349
DYHC_EMENI 4344
PKD1_HUMAN 4303
DYHC_SCHPO 4196
DYHC_YEAST 4092
RRPA_CVH22 4085
RRPL_DUGBV 4036
A.5 Statistics for journal citations
Total number of journals cited in this release of SWISS-PROT: 1011
A.5.1 Table of the frequency of journal citations
Journals cited 1x: 381
2x: 130
3x: 84
4x: 46
5x: 39
6x: 23
7x: 15
8x: 15
9x: 14
10x: 14
11- 20x: 75
21- 50x: 71
51-100x: 24
>100x: 80
A.5.2 List of the most cited journals in SWISS-PROT
Nb Citations Journal abbreviation
-- --------- ----------------------------------
1 6683 J. Biol. Chem.
2 4031 Proc. Natl. Acad. Sci. U.S.A.
3 3434 Nucleic Acids Res.
4 2868 J. Bacteriol.
5 2714 Gene
6 2162 FEBS Lett.
7 2046 Eur. J. Biochem.
8 1915 Biochem. Biophys. Res. Commun.
9 1888 Biochemistry
10 1788 EMBO J.
11 1684 Nature
12 1542 Biochim. Biophys. Acta
13 1462 J. Mol. Biol.
14 1321 Cell
15 1240 Mol. Cell. Biol.
16 1042 Genomics
17 999 Mol. Gen. Genet.
18 987 Plant Mol. Biol.
19 956 Biochem. J.
20 867 Science
21 828 Mol. Microbiol.
22 786 Virology
23 714 J. Biochem.
24 534 J. Virol.
25 487 Yeast
26 485 J. Cell Biol.
27 465 Plant Physiol.
28 465 J. Gen. Virol.
29 437 Hum. Mol. Genet.
30 427 Genes Dev.
31 398 Hum. Mutat.
32 371 J. Immunol.
33 367 Arch. Biochem. Biophys.
34 348 Infect. Immun.
35 346 Oncogene
36 336 Structure
37 329 Curr. Genet.
38 311 Mol. Biochem. Parasitol.
39 307 FEMS Microbiol. Lett.
40 307 Am. J. Hum. Genet.
41 301 Nat. Genet.
42 267 Development
43 265 Biol. Chem. Hoppe-Seyler
44 256 Microbiology
45 252 J. Clin. Invest.
46 250 Mol. Endocrinol.
47 249 Nat. Struct. Biol.
48 234 J. Mol. Evol.
49 233 Hum. Genet.
50 231 Genetics
51 222 J. Gen. Microbiol.
52 213 Hoppe-Seyler's Z. Physiol. Chem.
53 206 DNA Cell Biol.
54 204 Appl. Environ. Microbiol.
55 196 Protein Sci.
56 193 J. Exp. Med.
57 193 Blood
58 189 Dev. Biol.
59 184 Neuron
60 164 Immunogenetics
61 152 DNA Seq.
62 152 DNA
63 151 Endocrinology
64 140 Plant Cell
65 132 Cancer Res.
66 125 Plant J.
67 119 Mol. Biol. Evol.
68 118 Brain Res. Mol. Brain Res.
69 117 Mech. Dev.
70 117 J. Neurochem.
71 117 Biochimie
72 116 Hemoglobin
73 116 Bioorg. Khim.
74 115 Acta Crystallogr. D
75 113 Comp. Biochem. Physiol.
76 111 Virus Res.
77 110 Agric. Biol. Chem.
78 106 Mamm. Genome
79 106 J. Neurosci.
80 103 Biosci. Biotechnol. Biochem.
========================================================================
APPENDIX B: RELATIONSHIPS BETWEEN SWISS-PROT AND SOME BIOMOLECULAR
DATABASES
The current status of the relationships (cross-references) between
SWISS-PROT and some biomolecular databases is shown in the following
schematic:
***********************
* EMBL Nucleotide *
* Sequence Database *
* [EBI] *
***********************
^ ^ ^ ^ ^ ^ ^ ^ ^
****************** | | | I | | | | | **********************
* FlyBase * <-------+ | | I | | | | +-------> * MGD [Mouse] *
****************** | | | I | | | | | **********************
| | | I | | | | |
****************** | | | I | | | | | **********************
* SubtiList * <---------+ | I | | | +---------> * GCRDb [7TM recep.] *
* [B.subtilis] * | | | I | | | | | **********************
****************** | | | I | | | | |
| | | I | | | | | **********************
****************** | | | I | | +-----------> * EcoGene [E.coli] *
* Mendel [Plant] * <-----+ | | | I | | | | | **********************
****************** | | | | I | | | | |
| | | | I | | | | | **********************
****************** | | | | I +---------------> * SGD [Yeast] *
* MaizeDb * <-----------+ I | | | | | **********************
* [Zea mays] * | | | | I | | | | |
****************** | | | | I | | | | | **********************
| | | | I | +-------------> * DictyDB [D.disco.] *
****************** | | | | I | | | | | **********************
* WormPep * | | | | I | | | | |
* [C.elegans] * <---+ | | | | I | | | | | **********************
****************** | | | | | I | | | | | +-----> * ENZYME [Nomencl.] *
| | | | | I | | | | | | **********************
****************** | v v v v v v v v v v v v
* REBASE * ************************* **********************
* [Restriction * <-- * SWISS-PROT * ----> * OMIM [Human] *
* enzymes] * * Protein Sequence * **********************
****************** * Data Bank *
************************* **********************
****************** ^ ^ ^ ^ ^ ^ ^ | ^ ^ ^ * ECO2DBASE [2D] *
* StyGene * | | | | | | | | | | +--------> **********************
* [S.typhimurium]* <----+ | | | | | | | | |
****************** | | | | | | | | | **********************
| | | | | | | | +----------> * Maize-2DPAGE [2D] *
****************** | | | | | | | | **********************
* TRANSFAC * <------+ | | | | | | |
****************** | | | | | | | **********************
| | | | | | +------------> * SWISS-2DPAGE [2D] *
****************** | | | | | | **********************
* Harefield [2D] * <--------+ | | | | |
****************** | | | | | **********************
| | | | +--------------> * Aarhus/Ghent [2D] *
****************** | | | | **********************
* PROSITE * | | | |
* [Patterns and * <----------+ | | +----------------> **********************
* profiles] * | | * YEPD [Yeast] [2D] *
****************** | +----------------+ **********************
| v |
| *********************** +-> **********************
+--------> * PDB [3D structures] * <----- * HSSP [3D similar.] *
*********************** **********************
=End=of=SWISS-PROT=release=38=notes=====================================
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