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:

     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 ( .

Brian Fristensky                | 
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