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TrEMBL release 22.0

Published October 1, 2002


                              TrEMBL Release Notes
                              Release 22, October 2002

    EMBL Outstation
    European Bioinformatics Institute (EBI)
    Wellcome Trust Genome Campus
    Hinxton
    Cambridge CB10 1SD
    United Kingdom

    Telephone: (+44 1223) 494 444
    Fax: (+44 1223) 494 468
    Electronic mail address: DATALIB@EBI.AC.UK
    WWW server: http://www.ebi.ac.uk/

    Swiss Institute of Bioinformatics (SIB)
    Centre Medical Universitaire
    1, rue Michel Servet
    1211 Geneva 4
    Switzerland

    Telephone: (+41 22) 702 50 50
    Fax: (+41 22) 702 58 58
    Electronic mail address: Amos.Bairoch@isb-sib.ch 
    WWW server: http://www.expasy.org/


    Acknowledgements

    TrEMBL has been prepared by:

    o  Philippe Aldebert, Nicola Althorpe, Rolf Apweiler, Daniel Barrell, 
       Kirsty Bates, Paul Browne, Daniel Barrell, Kirill Degtyarenko, 
       Gill Fraser, Alexander Fedetov, Andre Hackmann, Henning Hermjakob, 
       Alexander Kanapin, Youla Karavidopoulou, Paul Kersey, Ernst Kretschmann,
       Kati Laiho, Minna Lehvaslaiho, Michele Magrane, Maria Jesus Martin, 
       Michelle McHale, Virginie Mittard, Nicola Mulder, Claire O'Donovan, 
       John F. O'Rourke, Sandra Orchard, Astrid Rakow, Sandra van den Broek, 
       Eleanor Whitfield and Allyson Williams at the EMBL Outstation - 
       European Bioinformatics Institute (EBI) in Hinxton, UK;
    o  Amos Bairoch, Alexandre Gattiker, Isabelle Phan and Sandrine Pilbout 
       at the Swiss Institute of Bioinformatics in Geneva, Switzerland.

    Copyright Notice
    TrEMBL copyright (c) 2002 EMBL-EBI
    This manual and the database it accompanies may be copied and
    redistributed freely, without advance permission, provided
    that this copyright statement is reproduced with each copy.

    Citation

    If you  want to  cite  TrEMBL  in  a  publication  please  use  the
    following reference:


              Bairoch A., and Apweiler R.
              The SWISS-PROT protein sequence data bank and its supplement
              TrEMBL in 2000.
              Nucl. Acids Res. 28:45-48(2000).


                         1. Introduction


TrEMBL is a computer-annotated protein sequence database supplementing the
SWISS-PROT Protein Knowledgebase. TrEMBL contains the translations of
all coding sequences (CDS) present in the EMBL/GenBank/DDBJ Nucleotide 
Sequence Databases and also protein sequences extracted from the literature 
or submitted to SWISS-PROT, which are not yet integrated into SWISS-PROT. 
TrEMBL can be considered as a preliminary section of SWISS-PROT. For all 
TrEMBL entries which should finally be upgraded to the standard SWISS-PROT 
quality, SWISS-PROT accession numbers have been assigned.

                        2. Why a supplement to SWISS-PROT?

The ongoing gene sequencing and mapping projects have dramatically
increased the number of protein sequences to be incorporated into SWISS-PROT.
We do not want to dilute the quality standards of SWISS-PROT by incorporating
sequences without proper sequence analysis and annotation, but we do want to
make the sequences available as quickly as possible. TrEMBL achieves this 
second goal, and is a major step in the process of speeding up subsequent
upgrading of annotation to the standard SWISS-PROT quality.
To address the problem of redundancy, the translations of all coding
sequences (CDS) in the EMBL Nucleotide Sequence Database already included
in SWISS-PROT have been removed from TrEMBL.


                             3. The Release

This TrEMBL release was created from the EMBL Nucleotide Sequence Database
release 72 and contains 821'014 entries and 36'790'365 amino acids. To 
minimize redundancy, the translations of all coding sequences (CDS) in the 
EMBL Nucleotide Sequence Database already included in SWISS-PROT release 40 
and updates until 25.10.02 have been removed from TrEMBL release 22.

TrEMBL is split in two main sections: SP-TrEMBL and REM-TrEMBL:
SP-TrEMBL (SWISS-PROT TrEMBL) contains the entries (734'427) which should be
eventually incorporated into SWISS-PROT. SWISS-PROT accession numbers have 
been assigned for all SP-TrEMBL entries.

SP-TrEMBL is organized in subsections:

arc.dat (Archaea):                          1694 entries
arp.dat (Complete Archaeal proteomes):     32840 entries 
fun.dat (Fungi):                           19843 entries
hum.dat (Human):                           39753 entries
inv.dat (Invertebrates):                   84525 entries
mam.dat (Other Mammals):                   11880 entries
mhc.dat (MHC proteins):                     8701 entries
org.dat (Organelles):                      89635 entries
phg.dat (Bacteriophages):                   6585 entries
pln.dat (Plants):                          98105 entries
pro.dat (Prokaryotes):                     86915 entries
prp.dat (Complete Prokaryotic Proteomes): 161638 entries
rod.dat (Rodents):                         32982 entries
unc.dat (Unclassified):                      149 entries
vrl.dat (Viruses):                         85797 entries
vrt.dat (Other Vertebrates):               14095 entries
vrv.dat (Retroviruses):                    82256 entries

72'120 new entries have been integrated in SP-TrEMBL. The sequences of 
4357 SP-TrEMBL entries have been updated and the annotation has been 
updated in 334'435 entries.

In the document deleteac.txt, you will find a list of all accession numbers 
which were previously present in TrEMBL, but which have now been deleted from 
the database.

REM-TrEMBL (REMaining TrEMBL) contains the entries (86'587) that we do
not want to include in SWISS-PROT. REM-TrEMBL entries do not have SWISS-PROT
accession numbers. Instead the stable ID portion of the protein_id present
in the source EMBL/DDBJ/GenBank nucleotide sequence database entries is
used as the ID and accession number.This section is organized in six 
subsections:

   1) Immunoglobulins and T-cell receptors (Immuno.dat)
      Most REM-TrEMBL entries are  immunoglobulins and  T-cell receptors. We
      stopped entering immunoglobulins and T-cell receptors into SWISS-PROT,
      because we only want to keep  the  germ line gene derived translations 
      of these proteins in SWISS-PROT and not all known somatic recombinated
      variations of  these proteins.  We would like to  create a specialized 
      database  dealing  with  these  sequences  as a further  supplement to 
      SWISS-PROT  and  keep  only a  representative  cross-section of  these 
      proteins in SWISS-PROT.

   2) Synthetic sequences (Synth.dat)
      Another category of data, which will not be included in SWISS-PROT are
      synthetic sequences.  Again, we do not want to  leave these entries in
      TrEMBL. Ideally one should build a specialized database for artificial 
      sequences as a further supplement to SWISS-PROT.

   3) Patent application sequences (Patent.dat)
      A third  subsection consists of  coding sequences captured from patent
      applications.  A thorough  survey of  these  entries  have shown  that 
      apart from a rather small minority  (which in  most cases have already 
      been integrated in SWISS-PROT), most of these sequences contain either
      erroneous data or concern artificially generated sequences outside the 
      scope of SWISS-PROT.

   4) Small fragments (Smalls.dat)
      Another  subsection  consists of fragments  with less than eight amino
      acids.

   5) CDS not coding for real proteins (Pseudo.dat)
      This subsection consists of CDS translations where we have strong
      evidence to believe that these CDS are not coding for real proteins.
      
   6) Truncated proteins (Truncated.dat)
      The last subsection consists of truncated proteins which result from    
      events like mutations introducing a stop codon leading to the truncation
      of the protein product.

                4. Format Differences Between SWISS-PROT and TrEMBL

The format and conventions used by TrEMBL follow as closely as possible
that of SWISS-PROT. Hence, it is not necessary to produce an additional
user manual and extensive release notes for TrEMBL. The information given
in the SWISS-PROT release notes and user manual are in general valid for
TrEMBL. The differences are mentioned below.

The general structure of an entry is identical in SWISS-PROT and TrEMBL.
The data class used in TrEMBL (in the ID line) is always 'PRELIMINARY',
whereas in SWISS-PROT it is always 'STANDARD'.

Differences in line types present in SWISS-PROT and TrEMBL:

The ID line (IDentification):

The entry name used in SP-TrEMBL is the same as the Accession Number of the
entry. The entry name used in REM-TrEMBL is the stable part of the protein_id 
tagged to the corresponding CDS in the EMBL Nucleotide Sequence Database. 
'protein_id' stands for the "Protein Identification" number. It is a number 
that you will find in the feature table of the EMBL nucleotide sequence 
entries in a qualifier called "/protein_id" which is tagged to every CDS.

Example:

FT   CDS             339..1514
FT                   /codon_start=1
FT                   /db_xref="PID:g1256015"
FT                   /product="dystrobrevin-epsilon"
FT                   /protein_id="AAC50431.1"

The protein_id is defined as follows in the The DDBJ/EMBL/GenBank Feature Table 
Definition documentation
Qualifier          /protein_id
Definition         Protein Identifier, issued by International collaborators.
                   This qualifier consists of a stable ID portion (3+5 format
                   with 3 position letters and 5 numbers) plus a version
                   number after the decimal point.
                   
Value format       <identifier>
Example            /protein_id="AAA12345.1"
Comment            When the protein sequence encoded by the CDS changes, only
                   the version number of the /protein_id value is incremented.
                   The stable part of the /protein_id remains unchanged and 
                   as a result will permanently be associated with a given
                   protein. This qualifier is valid only on CDS features 
                   which translate into a valid protein.                                   


The DT line (DaTe)

The format of the DT lines that serve to indicate when an entry was
created and updated are identical to that defined in SWISS-PROT; but the
DT lines in TrEMBL refer to the TrEMBL release. The difference is
shown in the example below.

    DT lines in a SWISS-PROT entry:

    DT   01-JAN-1988 (Rel. 06, Created)
    DT   01-JUL-1989 (Rel. 11, Last sequence update)
    DT   01-AUG-1992 (Rel. 23, Last annotation update)

    DT lines in a TrEMBL entry:

    DT   01-NOV-1996 (TrEMBLrel. 01, Created)
    DT   01-NOV-1996 (TrEMBLrel. 01, Last sequence update)
    DT   01-FEB-1997 (TrEMBLrel. 02, Last annotation update)

                5. Weekly updates of TrEMBL and non-redundant data sets

Weekly cumulative updates of TrEMBL are available by anonymous FTP and
from the EBI SRS server.

We also produce every week a complete non-redundant protein sequence 
collection by providing three compressed files (these are in the directory 
/pub/databases/sp_tr_nrdb on the EBI FTP server and in databases/sp_tr_nrdb
on the ExPASy server): sprot.dat.gz, trembl.dat.gz and trembl_new.dat.gz.
This set of non-redundant files is especially important for two types of 
users:
(i) Managers of similarity search services. They can now provide what is 
currently the most comprehensive and non-redundant data set of protein 
sequences.
(ii) Anybody wanting to update their full copy of SWISS-PROT + TrEMBL to 
their own schedule without having to wait for full releases of SWISS-PROT
or TrEMBL.

We have also introduced Varsplic Expand which is a program to generate
"expanded" sequences from SWISS-PROT and TrEMBL records i.e. sequences 
including the variants specified by the varsplic, variant and conflict 
annotations. New records are produced in either pseudo-SWISS-PROT or 
FASTA format for each specified variant. More information and the data is 
available at ftp://ftp.ebi.ac.uk/pub/databases/sp_tr_nrdb/

                6. Access/Data Distribution

FTP server:     ftp.ebi.ac.uk/pub/databases/trembl
SRS server:     http://srs.ebi.ac.uk/

TrEMBL is also available on the SWISS-PROT CD-ROM.
SWISS-PROT + TrEMBL is searchable on the following servers at the EBI:

FASTA3  (http://www.ebi.ac.uk/fasta33/)
BLAST2  (http://www.ebi.ac.uk/blast2/)
Bic_sw  (http://www.ebi.ac.uk/bic_sw/)
Scanps  (http://www.ebi.ac.uk/scanps/)
MPSrch  (http://www.ebi.ac.uk/MPsrch/)
	
For each TrEMBL release, a synchronized version of the concurrent SWISS-PROT 
release is distributed at ftp.ebi.ac.uk/pub/databases/trembl/swissprot/

	7. Planned changes


7.1 Evidence tags:

    We are continuing with the introduction of evidence tags to SWISS-PROT and 
    TrEMBL entries. The aim of this is to allow users to see where data items 
    came from and to enable SWISS-PROT staff to automatically update data if 
    the underlying evidence changes. This is ongoing internally and we hope 
    to provide a public version in 2002. For more information, 
    please see 
    ftp://ftp.ebi.ac.uk/pub/databases/trembl/evidenceDocumentation.html
    We would welcome any feedback from the user community.

7.2 Conversion of TrEMBL to mixed case:

    Most of the DE (DEscription), GN (Gene Name), RC (Reference Comment) 
    and CC (Comment) lines have been converted to mixed case internally. The 
    conversion is ongoing and will be made public as the conversion of each 
    line type reaches a satisfactory stage. A mixed case version of the DE 
    line was made public in last release.

7.3 Version of TrEMBL in XML format:
    
    A pre-prelease version of TrEMBL in XML format has been developed and is 
    provided with this release of TrEMBL.This will be provided in the future 
    for SWISS-PROT as well. More information is available at 
    http://www.ebi.ac.uk/swissprot/SP-ML and the data can be downloaded
    from ftp://ftp.ebi.ac.uk/pub/databases/trembl/xml
    We would welcome any feedback from the user community.