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TrEMBL release 4.0

Published July 1, 1997


                              TREMBL Release Notes
                              Release 4, Jul 1997


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

    Telephone: (+44 1223) 494 400
    Fax: (+44 1223) 494 468
    Electronic mail address: DATALIB@EBI.AC.UK
    WWW server: http://www.ebi.ac.uk/

    Amos Bairoch
    Medical Biochemistry Department
    Centre Medical Universitaire
    1211 Geneva 4
    Switzerland

    Telephone: (+41 22) 784 40 82
    Fax: (+41 22) 702 55 02
    Electronic mail address: BAIROCH@CMU.UNIGE.CH
    WWW server: http://expasy.hcuge.ch/

    Acknowledgements

    TREMBL has been prepared by:

    o  Rolf Apweiler, Sergio Contrino, Vivien Junker, Stephanie Kappus,
       Fiona Lang, Michele Magrane, Maria Jesus Martin, Nicoletta
       Mitaritonna and Claire O'Donovan at the EMBL Outstation - European
       Bioinformatics Institute (EBI) in Hinxton, UK;
    o  Amos Bairoch and Alain Gateau at the Medical Biochemistry Department
       of the University of Geneva, Switzerland.

    Notes

    This manual and the database it accompanies may be copied and
    redistributed freely, without advance permission, provided
    that this 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.
              Nucleic Acids Res. 25:31-26(1997).


                         1. Introduction


TREMBL is a computer-annotated protein sequence database supplementing the
SWISS-PROT Protein Sequence Data Bank. 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 genome 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.

We name this supplement TREMBL (TRanslation from EMBL), since the tools
used to create the translations of the CDS are based on the program
'trembl' written by Thure Etzold at the EMBL.


                             3. The Release

This TREMBL release is created from the EMBL Nucleotide Sequence Database
release 51 and contains 139'208 sequence entries, comprising 37'836'288 amino
acids. To minimize redundancy, the translations of all coding sequences (CDS)
in the EMBL Nucleotide Sequence Database already included in SWISS-PROT Release
34 and in SWISS-PROT updates by 21.7. have been removed from TREMBL release 4.

TREMBL is split in two main sections; SP-TREMBL and REM-TREMBL:

SP-TREMBL (SWISS-PROT TREMBL) contains the entries (116'769) 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:

fun.dat (Fungi):                3757 entries
hum.dat (Human):                5605 entries
inv.dat (Invertebrates):       15940 entries
mam.dat (Other Mammals):        2081 entries
mhc.dat (MHC proteins):         2694 entries
org.dat (Organelles):           8213 entries
phg.dat (Bacteriophages):        961 entries
pln.dat (Plants):               7776 entries
pro.dat (Prokaryotes):         26576 entries
rod.dat (Rodents):              5551 entries
unc.dat (Unclassified):          279 entries
vrl.dat (Viruses):             34508 entries
vrt.dat (Other Vertebrates):    2828 entries

REM-TREMBL (REMaining TREMBL) contains the entries (22'439) that we do
not want to include in SWISS-PROT.REM-TREMBL entries have no accession
numbers. This section is organized in five subsections:

   1) Immunoglobulins and T-cell receptors
      Most REM-TREMBL entries will be 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
      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
      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  contains  either
      erroneous data or concern artificially generated sequences outside the
      scope of SWISS-PROT.

   4) Small fragments
      Another  subsection consists  of fragments with less than seven amino
      acids.

   5) CDS not coding for real proteins
      The last subsection consists of CDS translations where we have strong
      evidence to believe that these CDS are not coding for real proteins.



                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 PID tagged to the
corresponding CDS in the EMBL Nucleotide Sequence Database. 'PID' stands for
the "Protein IDentification" number. It is a number that you will find in
EMBL nucleotide sequence entries in a qualifier called "/db_xref" which is
tagged to every CDS in the nucleotide database. Example:

   FT   CDS            54..1382
   FT                  /note="ribulose-1,5-bisphosphate carboxylase/
   FT                  oxygenase activase precursor"
   FT                  /db_xref="PID:g1006835"

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 are referring 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

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


                6. Access/Data Distribution

FTP server:     ftp.ebi.ac.uk/pub/databases/trembl
SRS server:     http://srs.ebi.ac.uk:5000/

TREMBL is also available on the SWISS-PROT CD-ROM.
SP-TREMBL is searchable on the FASTA server of the EBI and will be soon
searchable on the BLITZ server of the EBI.