Software to Parse Feature Table

frist at ccu.umanitoba.ca frist at ccu.umanitoba.ca
Thu Sep 16 16:13:18 EST 1993


In article <1993Sep16.155605.115532 at embl-heidelberg.de> etzold at embl-heidelberg.de writes:
>In article <1993Sep16.002128.44 at immunbio.mpg.de>, GARTMANN at IMMUNBIO.MPG.DE (Christoph Gartmann) writes:
>>> What software exists that can actually parse the (eminently parsible)
>>> joint features table format?  Please post reviews of programs you have
>>> used, or mail me directly and I will summarize.
>>> 
>> 
>> With Thure Etzold's SRS this can be done very easily.
>> 
>
>..i wish it could  - SRS can parse the feature table but so far only sequence
>ranges can be processed, ie, "123..345" - so from databanks like swissprot,
>PIR (yes PIR...) all features can be extracted automatically; the "join" and
>"complement" location commands of embl and genbank CANNOT be processed - however
>someone is working on it right now ...joins with fragments from different
>entries will be supported as well...however one can still try and get CDS's 
>from the nucleotide databanks - on average >50% will be processed ...depending
>on the age and the organism source of the entries
>
>thure etzold
The FEATURES program of the XYLEM package implements ALL elements of the
Feature Table syntax as defined in:

     DDBJ/EMBL/GenBank 
     Feature Table Definition (Version 1.04)  
     Sept. 1, 1992

This includes all operators such as join(), replace(), complement() etc.,
all operators, join()'s across many entries, and reference to features
by the /label= fields, as well as other qualifier fields. A paper has
been submitted and is currently under review. 

XYLEM may be obtained by anonymous FTP to the directory psgendb at
ftp.cc.umanitoba.ca (130.179.16.8) .

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