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TrEMBL release 2.0

Published February 1, 1997


                            TREMBL Release Notes
                            Release 2, February 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 49 and contains 116'379 sequence entries, comprising 31'293'053 
amino acids.


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

SP-TREMBL (SWISS-PROT TREMBL) contains the entries (96'757) 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):                3108 entries
hum.dat (Human):                4541 entries
inv.dat (Invertebrates):       13269 entries
mam.dat (Other Mammals):        1740 entries
mhc.dat (MHC proteins):         2307 entries
org.dat (Organelles):           6705 entries
phg.dat (Bacteriophages):        884 entries
pln.dat (Plants):               5699 entries
pro.dat (Prokaryotes):         23331 entries
rod.dat (Rodents):              4769 entries
vrl.dat (Viruses):             28150 entries
vrt.dat (Other Vertebrates):    2254 entries



REM-TREMBL (REMaining TREMBL) contains the entries (19'622) 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 sequence  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)