NCBI Server Format --> FASTA converter

Keith Robison robison1 at husc10.harvard.edu
Sun Oct 4 13:26:21 EST 1992


dab at ray.nlm.nih.gov (Dennis Benson) writes:

>robison1 at husc10.harvard.edu (Keith Robison) writes:
>: 
>: >Does someone already have a program to convert the results of a
>: >NCBI Sequence Server Query into FASTA format?  
>: 

>I also wonder whether as an interim solution, a FASTA type output option
>would take care of some of your needs, ie, do you need all of a PIR
>record in PIR format or is your principal need to get an identifier line
>and the sequence itself.  It would be easy to have a field in the mail
>message 'FASTA yes' or just  'FASTA' and have the program return just
>the FASTA-formatted sequence for any of the databases.

	I won't claim to speak for everyone, but I think this would
be an excellent _permanent_ option.  In my own work, a major reason
for my queries is to get the sequences for use in multiple alignments
and further queries, and so conversion to FASTA format is often my first
operation (since FASTA is probably the most accepted format for analysis
programs).  Actually, being able to specify the return format (FASTA, GCG,
etc) would probably be a feature many people would appreciate.

Keith Robison
Harvard University
Department of Cellular & Developmental Biology
Department of Genetics / HHMI

robison at ribo.harvard.edu 


P.S. -- I (and I suspect many others) would appreciate any suggestions
        for clever UNIX methods to strip out the header on the query returns.




More information about the Bio-soft mailing list