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Swiss-Prot release 9.0

Published December 1, 1988


             SWISS-PROT RELEASE 9.0 RELEASE NOTES


   Date:     December 1, 1988
   Author:   A. Bairoch


                         1. INTRODUCTION

   1.1  Evolution

   Release 9.0  of SWISS-PROT  contains 8702 sequence entries,
   comprising  2'498'140  amino  acids  abstracted  from  8735
   references. This represents an increase of 12% over release
   8.0. The  recent growth  of the  data  bank  is  summarised
   below:

   Release    Date   Number of entries     Nb of amino acids

   3.0        11/86               4160               969 641
   4.0        04/87               4387             1 036 010
   5.0        09/87               5205             1 327 683
   6.0        01/88               6102             1 653 982
   7.0        04/88               6821             1 885 771
   8.0        08/88               7724             2 224 465
   9.0        11/88               8702             2 498 140


   1.2  Source of data

   Release 9.0  has been  updated using  protein sequence data
   from  release  17.0  of  the  PIR  (Protein  Identification
   Resource) protein  data bank,  as well  as  translation  of
   nucleotide sequence  data from  release 17.0  of  the  EMBL
   nucleotide sequence Data Library.

   As an  indication to the source of the sequence data in the
   SWISS-PROT data bank we list here the statistics concerning
   the DR (Databank Reference) pointer lines:

   Entries with pointer(s) to only PIR entri(es):          3049
   Entries with pointer(s) to only EMBL entri(es):         2640
   Entries with pointer(s) to both EMBL and PIR entri(es): 2532
   Entries with no pointers lines (entered in house):       481


   2. Description  of the  changes made  to  SWISS-PROT  since
      release 8

   2.1  Sequences and annotations

   Some 978  new sequences  have been  added  since  the  last
   release, the sequence data of 111 existing entries has been
   updated and  the annotations  of  1622  entries  have  been
   revised. In  particular we  have used  reviews articles  to
   update the  annotations of the following groups or families
   of proteins:

        Acidic ribosomal proteins
        Adipokinetic hormone family
        ATP synthase subunits
        Bacterial histone-like DNA-binding proteins
        Bombesin-like peptides family
        Chaperonins
        Cholecystokinin/gastrin family
        Ferredoxins
        G-protein coupled receptors
        Histones H2A
        Histones H4
        HIV/SIV viruses proteins
        Homeobox proteins
        Integrins alpha chains
        Intermediate filaments
        Myosin heavy chains
        Myosin light chains
        Ovomucoids
        Oxytocin/vasopressin family
        Potato inhibitor I family
        Prion protein
        Receptor tyrosine-protein kinase class II
        Receptor tyrosine-protein kinase class III
        Ribonucleoproteins
        Serine carboxypeptidases
        Silk moth chorion proteins
        Thiol proteases inhibitors


   2.2  Cross-references to the HIV Sequence Database

   Starting with  release 9  we have added cross-references to
   entries in  the Human  Retroviruses and AIDS compilation of
   nucleic   and    amino   acid   sequences   (HIV   Sequence
   Database)(1). An  example of  a DR  line pointing to an HIV
   entry is shown here:

   DR   HIV; M15654; 3ORF$BH102.


   2.3  New topic for the comments (CC) line type

   As of  release 9  we have  added  a  new  'topic'  for  the
   comments (CC) line-type: ALTERNATIVE SPLICING which is used
   to describe  the existence  of related  protein sequence(s)
   produced by alternative splicing of the same gene(s).

   Example of its usage:

   CC   -!- ALTERNATIVE SPLICING: SKELETAL MUSCLE AND FIBROBLAST
   CC       TROPOMYOSINS ARE OBTAINED BY ALTERNATIVE MRNA SPLICING.


   3. THE NEXT RELEASE

   SWISS-PROT release 10.0 will be available in February 1989.
   We plan to upgrade the OC lines so as to add at least a few
   level of  taxonomic nodes  (currently  only  the  top-node:
   viridae, prokaryota or eukaryota is available).


   4. WE NEED YOUR HELP !

   We welcome any feedback from our users. We especially would
   appreciate that  you notify  us if  you find that sequences
   belonging to  your field  of expertise are missing from the
   data  bank.  We  also  would  like  to  be  notified  about
   annotations to  be updated,  as for example if the function
   of  a   protein  has   been  clarified   or  if  new  post-
   translational information has become available.


   ____________________
   1  The HIV  Sequence Database  is edited  by G. Myers, A.B.
      Rabson,  S.F.   Josephs,  T.F.   Smith,  F.  Wong-Staal;
      published by  the  Theoretical  Biology  and  Biophysics
      Group T-10 at Los Alamos National Laboratory; and funded
      by the AIDS program of the National Institute of Allergy
      and Infectious Diseases through an interagency agreement
      with the United States Department of Energy.


   APPENDIX A: DISKS FOR SWISS-PROT

   -  Release 9  is the first release to be available on a CD-
      ROM disk.
   -  Starting with  release 9  we have  stopped  distributing
      SWISS-PROT on 360 Kb disks.

   A.1  IBM PC/AT 1.2 Mb disks

   SWISS-PROT is  stored on  ten 1.2  Mb disks.  Each of these
   disk  contains   a  single   bulk  file   (PROT9_01.BLK  to
   PROT9_10.BLK):

   Disk     First sequence        Last Sequence
    1       16K$TRVPS             CAS2$BOVIN
    2       CAS2$SHEEP            CYSE$ECOLI
    3       CYSP$MOUSE            GENK$ECOLI
    4       GENL$ECOLI            IBB3$SOYBN
    5       IBB4$MACAX            LPID$EDWTA
    6       LPIV$ECOLI            PA21$PIG
    7       PA21$PSEAU            RENI$RAT
    8       RENS$MOUSE            TOLC$ECOLI
    9       TOLL$DROME            VSI1$REOV1
   10       VSI1$REOV2            ZEB2$MAIZE

   A.2  IBM PS/2 1.4 Mb disks

   The number  and content  of the  1.4 Mb  disks for the PS/2
   systems are  exactly identical to those of the 1.2 Mb disks
   (see above).



   APPENDIX B: SOME STATISTICS

   B.1  Amino acid composition



        COMPOSITION IN PERCENT FOR THE COMPLETE DATA BANK

   Ala (A) 7.75   Gln (Q) 4.10   Leu (L) 9.06   Ser (S) 7.01
   Arg (R) 5.15   Glu (E) 6.17   Lys (K) 5.89   Thr (T) 5.84
   Asn (N) 4.37   Gly (G) 7.32   Met (M) 2.29   Trp (W) 1.36
   Asp (D) 5.19   His (H) 2.28   Phe (F) 3.94   Tyr (Y) 3.23
   Cys (C) 1.90   Ile (I) 5.32   Pro (P) 5.17   Val (V) 6.51

   Asx (B) 0.02   Glx (Z) 0.01   Xaa (X) 0.03


      CLASSIFICATION OF THE AMINO ACIDS BY THEIR FREQUENCY

   Leu, Ala, Gly, Ser, Val, Glu, Lys, Thr, Ile, Asp, Pro, Arg,
   Asn, Gln, Phe, Tyr, Met, His, Cys, Trp


   B.2   Repartition of  the sequences  by their  organism  of
         origin

   Total number  of species represented in this release of the
   data bank: 1345

   Species represented 1x:  700
                       2x:  276
                       3x:  155
                       4x:   88
                       5x:   48
                       6x:   43
                       7x:   23
                       8x:   28
                       9x:   24
                      10x:   10
                     >10x:   83



              TABLE OF THE MOST REPRESENTED SPECIES

   795: HUMAN       142: DROME       69: SALTY       59: VACCV
   703: ECOLI       141: CHICK       68: BPT4        54: BPT7
   452: MOUSE       129: RABIT       67: MAIZE       52: MARPO
   356: RAT         116: PIG         62: LAMBD       50: WHEAT
   297: YEAST        85: XENLA           TOBAC
   264: BOVIN        81: BACSU       59: EPBAR


   B.3  Repartition of the sequences by size

   From   To  Number            From   To   Number
      1-  50     487            1001-1100       54
     51- 100    1179            1101-1200       34
    101- 150    1893            1201-1300       29
    151- 200     938            1301-1400       21
    201- 250     661            1401-1500       13
    251- 300     554            1501-1600        4
    301- 350     492            1601-1700       10
    351- 400     483            1701-1800        8
    401- 450     354            1801-1900        6
    451- 500     387            1901-2000        3
    501- 550     327            >2000           43
    551- 600     176
    601- 650     135            Currently the two largest sequences are:
    651- 700      87            APB$HUMAN   4563 a.a.
    701- 750      82            APOA$HUMAN  4548 a.a.
    751- 800      61
    801- 850      52
    851- 900      68
    901- 950      30
    951-1000      31