*sequence analysis programs for IBM PC

Dan Jacobson danj at WELCHGATE.WELCH.JHU.EDU
Thu Apr 2 16:05:51 EST 1992

Anne Marie Quinn asks:

>Would anyone care to recommend programs for genetic
>sequence analysis on an IBM PC?  We would like a 
>windows interface to do restriction mapping, sequence 
>alignment and fragment assembly... (*AND*) a client to
>transfer sequence to and results from NCBI for blast searches!

Hi Anne Marie,

Hmm you`ve asked quite a few questions in two sentences.

I'll see what I can do -

For general sequence analysis packages for the IBM-PC
FSAP and Seqaid come to mind - they will both do restriction
maps and sequence alignment (of 2 sequences).  Comap is good
at helping you build restriction maps from digestion data (ie
bands on a gel), marker is a fun little program for doing
restriction maps.

If you want to do MULTIPLE alignments on a pc - MACAW is probably
the best way to go, there are others - clustal and esee.

There are some great shell scripts for submitting sequences to
the variuos databases for fasta or blast searches for Unix or
Vax/VMS systems - I don't know of any off hand that submitt
sequences to the mail servers from a PC though.

Contig assembly is a little tougher - I think COMAP may have
a new b-test function on this that Kay Hoffman is working on
but my memory is a bit fuzzy on that.

If you have protein anaylis to do PROGRAPH is probably the best
I've seen for the PC.

All these programs are findable by Archie - if you want I'll
send out locations from where they can be ftp'ed but if you
can do the archie search on what you want that'll save me some time.  
At any rate they are all at ftp.bio.indiana.edu or nic.funet.fi
or ftp.bchs.uh.edu (Kudoes to Don Gilbert, Rob Harper and Dan 
Davison respectively).  The exception is MACAW which I believe
is only at ncbi.nlm.nih.gov  .

Hope this helps,

Dan Jacobosn

danj at welchgate.welch.jhu.edu


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