FASTA style database in SRS (one solution!)

Ramu Chenna chenna at embl-heidelberg.de
Thu Oct 30 11:39:17 EST 1997


Hello 'All the impatient'

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)


>/: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 AMP-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 and thank me !

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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