looking at local BLAST alignments

Thomas Isenbarger isen at molbio.mgh.harvard.edu
Wed Mar 19 15:32:47 EST 2003


I am using a local installation of the NCBI blastall program.  i have 
been playing around with the various output formats (command line switch 
-m).

What program is good for viewing the alignments output by locally 
installed blast?  The blast output breaks the alignments into blocks of 
60 characters and I would like to have all the alignment on a single 
line. Is there a blast parameter to use that can set this (line length)?

also, is it better to output a SeqAlign file (-O) and graphically view 
the ASN.1 output from that?  or XML (-m 9)?

I am using Mac OS X and I have the EMBOSS package installed.  I also 
have the X11 from apple installed, so if you could direct me to any OS X 
native programs (Cocoa or Carbon) or any unix EMBOSS or X11 programs 
that would be great.

is there a command line program that can be used to convert the blast 
output into a FASTA alignment (or other format) that can be imported in 
MacVector or Se-Al for Mac OS X?

Thank-you in advance,
Tom Isenbarger

isenATmolbioDOT.mghDOTharvardDOT.edu
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