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TrEMBL release 19.0

Published December 1, 2001


                              TrEMBL Release Notes
                              Release 19, December 2001

    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  Rolf Apweiler, Kirsty Bates, Margaret Biswas, Sergio Contrino, 
       Daniel Barrell, Kirill Degtyarenko, Wolfgang Fleischmann, Gill Fraser, 
       Henning Hermjakob, Kati Laiho, Alexander Kanapin, Youla Karavidopoulou, 
       Paul Kersey, Minna Lehvaslaiho, Michele Magrane, Maria Jesus Martin, 
       Virginie Mittard, Nicola Mulder, Claire O'Donovan, John F. O'Rourke, 
       Eleanor Whitfield and Allyson Williams at the EMBL Outstation - 
       European Bioinformatics Institute (EBI) in Hinxton, UK;
    o  Amos Bairoch, Alain Gateau, Isabelle Phan and Sandrine Pilbout at the 
       Swiss Institute of Bioinformatics in Geneva, Switzerland.

    Copyright Notice
    TrEMBL copyright (c) 2000 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 Nucleotide Sequence Database
not yet integrated in 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 fast 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 68 and updates until 16.11.01 and contains 636'825 entries 
and 184'332'036 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 13.12.01 have been 
removed from TrEMBL release 19

TrEMBL is split in two main sections: SP-TrEMBL and REM-TrEMBL:
SP-TrEMBL (SWISS-PROT TrEMBL) contains the entries (562'222) 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):                        1692 entries
arp.dat (Complete Archaeal proteomes):   19590 entries 
fun.dat (Fungi):                         13339 entries
hum.dat (Human):                         29064 entries
inv.dat (Invertebrates):                 60611 entries
mam.dat (Other Mammals):                  9724 entries
mhc.dat (MHC proteins):                   7434 entries
org.dat (Organelles):                    50792 entries
phg.dat (Bacteriophages):                 4368 entries
pln.dat (Plants):                        58841 entries
pro.dat (Prokaryotes):                   69426 entries
prp.dat (Complete Prokaryote Proteomes): 74477 entries
rod.dat (Rodents):                       24185 entries
unc.dat (Unclassified):                    252 entries
vrl.dat (Viruses):                       60309 entries
vrt.dat (Other Vertebrates):             11003 entries
vrv.dat (Retroviruses):                  67115 entries

80'772 new entries have been integrated in SP-TrEMBL. The sequences of 
1388 SP-TrEMBL entries have been updated and the annotation has been 
updated in 321'110 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 (74'603) that we do
not want to include in SWISS-PROT. REM-TrEMBL entries have no accession
numbers. 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 of TrEMBL.

We also recently introduced Varsplic Expand which is a program to generate
"expanded" sequences from SWISS-PROT 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/)
	

	7. Description of changes made to TrEMBL since release 18

7.1 Changes concerning cross-references (DR line)

    We have added crossreferences from TrEMBL to a number of new databases.

    7.1.1 MEROPS, the protease database, available at http://www.merops.co.uk
    
    7.1.2 ANU-2DPAGE, the Australian National University Two-Dimensional 
          Polyacrylamide Gel Electrophoresis Database, available at
          http://semele.anu.edu.au/2d/2d.html
   
    7.1.3 PHCI-2DPAGE, the two-dimensional polyacrylamide gel electrophoresis 
          database at Universidad Complutense de Madrid, available at
          http://babbage.csc.ucm.es/2d/2d.html

    7.1.4 PMMA-2DPAGE, the Purkyne Military Medical Academy 2D-PAGE database,
          available at http://www.pmma.pmfhk.cz/2d/2d.html

    7.1.5 Siena-2DPAGE, the 2D-PAGE database from the Department of Molecular
          Biology, University of Siena, Italy, available at
          http://www.bio-mol.unisi.it/2d/2d.html

A list of all crossreferences in TrEMBL to other databases is provided below:
EMBL
PIR
PDB
HSSP
MEROPS
REBASE
TRANSFAC
Aarhus/Ghent-2DPAGE
ANU-2DPAGE
COMPLUYEAST-2DPAGE
PHCI-2DPAGE
PMMA-2DPAGE
Siena-2DPAGE
FlyBase
Leproma
MIM
MGD
MypuList
SGD
SubtiList
TIGR
TubercuList
WormPep
ZFIN
InterPro
Pfam
PRINTS
ProDom
SMART
PROSITE

7.2 New database divisions:

    Three new database divisions were created as previously announced 
    to reflect the specialised attention we are giving to complete 
    proteomes and the HAMAP project. The new viral division is for 
    operational reasons:

    7.2.1 New database division 'arp'
	  It will contain archaeal complete proteome entries.
    7.2.2 New database division 'prp'
	  It will contain bacterial complete proteome entries.
    7.2.3 New database division 'vrv'
	  It will contain retrovirus entries.


	8. Planned changes


8.1 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 early 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.

8.2 Conversion of TrEMBL to mixed case:

    Most of the DE (DEscription), GN (Gene Name) and RC (Reference Comment) 
    lines is being converted to mixed case internally. The conversion is 
    ongoing and will be made public when ready.

8.3 Version of SWISS-PROT/TrEMBL in XML format:
    
    A distribution version of SWISS-PROT and TrEMBL in XML format is 
    being developed. The specifications of this new format will be described
    when it will be first implemented in TrEMBL.

8.4 Multiple RP lines:

    In the workreleases from release 19 onwards, there can be more than one 
    RP (Reference Position) line per reference in a TrEMBL entry. For more 
    information on this development, please read SWISS-PROT Protein 
    Knowledgebase Release Notes 40 at http://www.expasy.org/sprot/relnotes