UniProtKB/TrEMBL - Old Release Notes

N.B. From release 27, the UniProtKB/TrEMBL release notes are included in the UniProt release notes.

                              UniProtKB/TrEMBL Release Notes

                              Release 23, March 2003

    EMBL Outstation

    European Bioinformatics Institute (EBI)

    Wellcome Trust Genome Campus


    Cambridge CB10 1SD

    United Kingdom

    Telephone: (+44 1223) 494 444

    Fax: (+44 1223) 494 468

    Electronic mail address:

    WWW server:

    Swiss Institute of Bioinformatics (SIB)

    Centre Medical Universitaire

    1, rue Michel Servet

    1211 Geneva 4


    Telephone: (+41 22) 702 50 50

    Fax: (+41 22) 702 58 58

    Electronic mail address: 

    WWW server:


    TrEMBL has been prepared by:

    o  Maria Jesus Martin, Claire O'Donovan, Nicola Althorpe, Rolf 

       Apweiler, Daniel Barrell, Kirsty Bates, Paul Browne, Daniel Barrell, 

       Kirill Degtyarenko, Gill Fraser, Alexander Fedetov, Andre Hackmann, 

       Alexander Kanapin, Youla Karavidopoulou, Paul Kersey, Ernst 

       Kretschmann, Kati Laiho, Minna Lehvaslaiho, Michele Magrane, Michelle 

       McHale, Virginie Mittard, Nicola Mulder, 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, Karine Michoud, Isabelle Phan and 

       Sandrine Pilbout at the Swiss Institute of Bioinformatics in Geneva, 


    Copyright Notice

    TrEMBL copyright (c) 2003 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.


    If you  want to  cite  UniProtKB/TrEMBL  in  a  publication  please  use  

    the following reference:

    Boeckmann B., Bairoch A., Apweiler R., Blatter M., Estreicher A.,

    Gasteiger E., Martin M.J., Michoud K., O'Donovan C., Phan I., 

    Pilbout S., and Schneider M. (2003)

    The Swiss-Prot protein knowledgebase and its supplement TrEMBL in 


    Nucleic Acids Res. 31:365-370.

                         1. Introduction

TrEMBL is a computer-annotated protein sequence database 

complementing 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. 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 complement 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 has been produced in synch with Swiss-Prot release 41. It 

was created from the EMBL Nucleotide Sequence Database release 73 and contains 

921'952 entries and 40'914'860 amino acids.

UniProtKB/TrEMBL is split in two main sections: SP-TrEMBL and REM-TrEMBL:

SP-TrEMBL (Swiss-Prot TrEMBL) contains the entries (830'525) which should 

be eventually incorporated into UniProtKB/Swiss-Prot. UniProtKB/Swiss-Prot accession numbers 

have been assigned for all SP-TrEMBL entries.

SP-TrEMBL is organized in subsections:

arc.dat (Archaea):                          1736 entries

arp.dat (Complete Archaeal proteomes):     31625 entries 

fun.dat (Fungi):                           15977 entries

hum.dat (Human):                           34880 entries

inv.dat (Invertebrates):                   79680 entries

mam.dat (Other Mammals):                   12223 entries

mhc.dat (MHC proteins):                     8813 entries

org.dat (Organelles):                      73538 entries

phg.dat (Bacteriophages):                   6448 entries

pln.dat (Plants):                          80929 entries

pro.dat (Prokaryotes):                     79736 entries

prp.dat (Complete Prokaryotic Proteomes): 181432 entries

rod.dat (Rodents):                         40143 entries

unc.dat (Unclassified):                      331 entries

vrl.dat (Viruses):                         82490 entries

vrt.dat (Other Vertebrates):               14889 entries

vrv.dat (Retroviruses):                    85655 entries

107'123 new entries have been integrated in SP-TrEMBL. The sequences of 

1713 SP-TrEMBL entries have been updated and the annotation has been 

updated in 252'549 entries.

In the document deleteac.txt, you will find a list of all accession numbers 

which were previously present in UniProtKB/TrEMBL, but which have now been deleted from 

the database.

REM-TrEMBL (REMaining TrEMBL) contains the entries (91'427) 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 


   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 UniProtKB/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


   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 UniProtKB/Swiss-Prot and UniProtKB/TrEMBL

The format and conventions used by TrEMBL follow as closely as possible

that of UniProtKB/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 UniProtKB/Swiss-Prot and UniProtKB/TrEMBL.

The data class used in UniProtKB/TrEMBL (in the ID line) is always 'PRELIMINARY',

whereas in UniProtKB/Swiss-Prot it is always 'STANDARD'.

Differences in line types present in UniProtKB/Swiss-Prot and UniProtKB/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.


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       

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 UniProtKB/TrEMBL refer to the TrEMBL release. The difference is

shown in the example below.

    DT lines in a UniProtKB/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 UniProtKB/TrEMBL entry:

    DT   01-NOV-1996 (TrEMBLrel. 01, Created)

    DT   01-NOV-1999 (TrEMBLrel. 12, Last sequence update)

    DT   28-FEB-2003 (TrEMBLrel. 23, Last annotation update)

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

5.1 UniProtKB/TrEMBL updates

Weekly cumulative updates of UniProtKB/TrEMBL are available by anonymous FTP and

from the EBI SRS server.

5.2 SPTr

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 


(i) Managers of similarity search services. They can now provide what is 

currently the most comprehensive and non-redundant data set of protein 


(ii) Anybody wanting to update their full copy of UniProtKB/Swiss-Prot + UniProtKB/TrEMBL to 

their own schedule without having to wait for full releases of UniProtKB/Swiss-Prot

or UniProtKB/TrEMBL.

5.3 XML

A version of UniProtKB/Swiss-Prot and UniProtKB/TrEMBL in XML format has been developed and is 

provided with this release. More information is available at and the data can be downloaded

from and

We would welcome any feedback from the user community.

5.4 Varsplic Expand

We also provide Varsplic Expand which is a program to generate

"expanded" sequences from UniProtKB/Swiss-Prot and UniProtKB/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

            6. Access/Data Distribution

FTP server:

SRS server:

UniProtKB/TrEMBL is also available on the UniProtKB/Swiss-Prot CD-ROM.

UniProtKB/Swiss-Prot + UniProtKB/TrEMBL is searchable on the following servers at the EBI:



Scanps  (

MPSrch  (


For each UniProtKB/TrEMBL release, a synchronized version of the concurrent UniProtKB/Swiss-Prot 

release is distributed at

    7. Description of changes made to TrEMBL since release 22.

7.1 Changes concerning cross-references (DR line)


  We have added cross-references from TrEMBL to a number of new databases.

  7.1.1 Schizosaccharomyces pombe GeneDB Prototype

  We have added cross-references to the Schizosaccharomyces pombe GeneDB 

  Prototype (available at 

  7.1.2 Genew

  We have added cross-references to the Human Gene Nomenclature Database Genew

  (available at

7.2 Changes concerning the Organelle (OG) line

The term Nucleomorph has been added which is the residual nucleus of an

algal endosymbiont that resides inside its host cell.

                      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 UniProtKB/Swiss-Prot staff to automatically update data if 

the underlying evidence changes. This is ongoing internally and the evidence 

tags are visible in the XML version of Swiss-Prot and TrEMBL.

For more information, please see

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), 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 release 21. The RC line is mixed case in this 


8.3 Version of SPTr in XML format:


We intend to provide an XML version of SPTr updated monthly

8.4 Reference Comment (RC) line topics may span lines

The RC (Reference Comment) line store comments relevant to the reference

cited, in currently 5 distinct topics: PLASMID, SPECIES, STRAIN, TISSUE and

TRANSPOSON. It is not always possible to list all information within one

line. Therefore we will allow multiple RC lines, in which one topic might

span over a line. Example:

RC   STRAIN=Various strains;

could become

RC   STRAIN=AZ.026, DC.005, GA.039, GA2181, IL.014, IN.018, KY.172, KY2.37,

RC   LA.013, MN.001, MNb027, MS.040, NY.016, OH.036, TN.173, TN2.38,

RC   UT.002, AL.012, AZ.180, MI.035, VA.015, and IL2.17;

8.5  New format of comment line (CC) topics

We are continuing a major overhaul of various comment line topics. We would

like the majority of the information stored to be usable by computer

programs (while remaining human-readable). We are therefore standardizing

the format of the topics. Please see Swiss-Prot release 41 relnotes for

further details.

8.6 Modifications concerning the feature table (FT line)

We are investigating a major effort in the annotation of posttranslational

modifications, which has an effect on various feature keys and feature

descriptions. Please see UniProtKB/Swiss-Prot release 41 relnotes for further details.

8.7  Extension of the entry name format

Currently UniProtKB/TrEMBL has it's accession number as the entry name. It is 

intended to extend this to have the accession number as the protein 

name component of the entry name (having elongated the mnemonic code 

from 4 characters to 6) and to assign the mnemonic species identification

code of at most 5 alphanumeric characters as Swiss-Prot currently does.