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 

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


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