: FASTA style database in SRS (one solution!)

chenna at embl-heidelberg.de chenna at embl-heidelberg.de
Fri Oct 31 08:52:28 EST 1997


Hello 'All the impatient'

(Looks like posting from embl does not reach propery, again
posting from dejanews!)

Many people asked about using the following fasta (???) format
database with SRS.


One of the solution is to convert it to swiss format and use it.
(Many other applications can also use this db, eg., gcg programs)


funnyFasta entries looks like this!

>/:swissnew|P80385|AAKG_RAT 5'-AMP-ACTIVATED PROTEIN KINASE, GAMMA-1 SUBUNIT

(AMPK GAMMA CHAIN).//:trembl|X95578|RNAMPKGAM_1 product : "AMP-activated
protein kinase gamma";	R.norvegicus mRNA for gamma subunit of
AMP-activated protein kinase //:gp|X95578|1185271 AM P-activated protein
kinase gamma [Rattus norvegicus]
MESVAAESAPAPENEHSQETPESNSSVYTTFMKSHRCYDLIPTSSKLVVFDTSLQVKKAF
FALVTNGVRAAPLWDSKKQSFVGMLTITDFINILHRYYKSALVQIYELEEHKIETWREVY




pickup the conversion program from


http://www.embl-heidelberg.de/~chenna/funnyFasta2swiss.is


and then


you can copy the syntax and structure files for this from embl srs server
to use with SRS.  They are  nrdb.i and nrdb.is (you know how to get them,
don't you?)


if you are converting a nuc database then change


  $SeqPrint:[format:swiss]   to


  $SeqPrint:[format:embl]


in the funnyFasta2swiss.is file.


I wrote funnyFasta2swiss.is  long time back and took time to locate it.


enjoy !


Ramu
_______________________________________________________________
Chenna Ramu; EMBL; Postfach 10.2209; 69012 Heidelberg; Germany.
Email: chenna at embl-heidelberg.de
   Url: http://www.embl-heidelberg.de/~chenna/
   Tel: (49) 6221 387530 (Off) ; Fax: (49) 6221 387517
______

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