ANNOUNCEMENT: Beta release of TREMBL, a supplement to SWISS-PROT

[Rolf Apweiler]

In article <4kdd6m$kfs at mserv1.dl.ac.uk>, Martin Hilbers <mph at dl.ac.uk> writes:
>Wow,
>
>Looks nice. But what is the relation between this TREMBL and the TREMBL
>produced by Thure Etzold in Heidelberg, which was also created from
>EMBL 46.0 and contains 169636 entries ?
>
>
>Martin

Hi Martin,

Thure Etzolds TREMBL and TREMBL done by SWISS-PROT are related. TREMBL done 
by SWISS-PROT is the successor or the next generation of Thures TREMBL.  
SWISS-PROT kept the name TREMBL for their Translation of EMBL CDS, since 
the tools used to create the translations of the CDS are based on the 
program 'trembl' written by Thure Etzold at the EMBL in Heidelberg.

So, what are the differences?
Thure translates all CDS in the EMBL nucleotide sequence database into 
TREMBL entries. 
TREMBL done by SWISS-PROT excludes all the entries which are already 
integrated in SWISS-PROT to make SWISS-PROT and TREMBL non-redundant.
Also, all TREMBL entries are in SWISS-PROT format
and SWISS-PROT merges TREMBL entries and adds computer generated 
annotation, references and cross-references to other databases.
So, the entries are quite different. An example see below.

In June the first official release of TREMBL done by SWISS-PROT will be 
available and at that stage Thures TREMBL will disappear. However, everybody 
who wants to generate a translation of all EMBL CDS as single entries can 
still use Thures program 'trembl' to do so; it will be distributed as 
part of SRS.

For more information see the release notes of TREMBL and SWISS-PROT or 
read:
              Bairoch A., and Apweiler R.
              The SWISS-PROT protein sequence data bank and its new
              supplement TREMBL.
              Nucleic Acids Res. 24:21-25(1996).


We hope this info helps.


Rolf Apweiler and Thure Etzold


Examples

Thures TREMBL entry:

ID   S64977_2  standard; PRT; 228 AA.
AC   S64977;
DR   EMBL; S64977; S64977.
DE   gene: "COII"; 
DE   COI=cytochrome oxidase subunit I...COIII=cytochrome oxidase subunit
DE   III [Drosophila simulans, Mitochondrial, 8 genes, 1990 nt]
OS   Drosophila simulans (fruit fly)
OC   Eukaryota; Animalia; Metazoa; Arthropoda; Uniramia; Insecta;
OC   Pterygota; Neoptera; Holometabola; Diptera; Brachycera;
OC   Cyclorrhapha; Schizophora; Drosophiloidea; Drosophilidae.
OG   Mitochondrion
FT   CDS             115..799
FT                   /note="Description: cytochrome oxidase subunit II"
FT                   /gene="COII"
FT                   /db_xref="FLYBASE:FBgn0012877"
FT                   /db_xref="PID:e87967"
FT                   /translation="MSTWANLGLQDSASPLMEQLIFFHDHALLILVMITVLVGYLMFML
FT                   FFNNYVNRFLLHGQLIEMIWTILPAIILLFIALPSLRLLYLLDEINEPSVTLKSIGHQW
FT                   YWSYEYSDFNNIEFDSYMIPTNELSIDGFRLLDVDNRVILPMNSQIRILVTAADVIHSW
FT                   TIPALGVKVDGTPGRLNQTNFFINRPGLFYGQCSEICGANHSFMPIVIESVPVNHFIKW
FT                   ISSNNS"
CC   translated using genetic code table "Invertebrate Mitochondrial"
SQ   Sequence   228 BP;
>S64977_2
MSTWANLGLQDSASPLMEQLIFFHDHALLILVMITVLVGYLMFMLFFNNYVNRFLLHGQL
IEMIWTILPAIILLFIALPSLRLLYLLDEINEPSVTLKSIGHQWYWSYEYSDFNNIEFDS
YMIPTNELSIDGFRLLDVDNRVILPMNSQIRILVTAADVIHSWTIPALGVKVDGTPGRLN
QTNFFINRPGLFYGQCSEICGANHSFMPIVIESVPVNHFIKWISSNNS


Corresponding SWISS-PROT TREMBL entry:

ID   E87967         PRELIMINARY;   PRT;   228 AA.
DT   26-MAR-1996 (EMBLREL. 46, CREATED)
DT   26-MAR-1996 (EMBLREL. 46, LAST SEQUENCE UPDATE)
DT   26-MAR-1996 (EMBLREL. 46, LAST ANNOTATION UPDATE)
DE   CYTOCHROME C OXIDASE POLYPEPTIDE II (EC 1.9.3.1).
GN   COII.
OS   DROSOPHILA SIMULANS (FRUIT FLY).
OG   MITOCHONDRION.
OC   EUKARYOTA; METAZOA; ARTHROPODA; INSECTA; DIPTERA.
RN   [1]
RP   SEQUENCE FROM N.A.
RX   MEDLINE; 93374296.
RA   KANEKO M., SATTA Y., MATSUURA E.T., CHIGUSA S.I.;
RL   GENET. RES. 61:195-204(1993).
CC   -!- CATALYTIC ACTIVITY: 4 FERROCYTOCHROME C + O(2) = 2 H(2)O + 4
CC       FERRICYTOCHROME C.
CC   -!- FUNCTION: SUBUNIT I AND II FORM THE FUNCTIONAL CORE OF THE ENZYME
CC       COMPLEX. ELECTRONS ORIGINATING IN CYTOCHROME C ARE TRANSFERRED VIA
CC       HEME A AND CU(A) TO THE BINUCLEAR CENTER FORMED BY HEME A3 AND
CC       CU(B). SUBUNIT II BINDS CU(A) AND CYTOCHROME C.
CC   -!- COFACTOR: COPPER A AND HEME GROUP.
CC   -!- SUBCELLULAR LOCATION: INTEGRAL MEMBRANE PROTEIN. (MITOCHONDRIAL).
CC   -!- SIMILARITY: TO OTHER MITOCHONDRIAL OR BACTERIAL COX2 SUBUNITS.
DR   EMBL; S64977; E87967; -.
DR   FLYBASE; FBGN0012877; DSIM\MT:COI.
DR   PROSITE; PS00078; COX2.
KW   MITOCHONDRION; OXIDOREDUCTASE; COPPER; TRANSMEMBRANE.
FT   METAL       196    196       COPPER A (PROBABLE).
FT   METAL       200    200       COPPER A (PROBABLE).
FT   METAL       204   >204       COPPER A (PROBABLE).
SQ   SEQUENCE   228 AA;  26160 MW;  0E17E9D6 CRC32;
     MSTWANLGLQ DSASPLMEQL IFFHDHALLI LVMITVLVGY LMFMLFFNNY VNRFLLHGQL
     IEMIWTILPA IILLFIALPS LRLLYLLDEI NEPSVTLKSI GHQWYWSYEY SDFNNIEFDS
     YMIPTNELSI DGFRLLDVDN RVILPMNSQI RILVTAADVI HSWTIPALGV KVDGTPGRLN
     QTNFFINRPG LFYGQCSEIC GANHSFMPIV IESVPVNHFI KWISSNNS
//