Hi Theodore,<br><br>For serious work, I don't recommend this, because you would really have to recalculate lamba and the gap penalties. For playing around, you can specify the matrix with -M. The easiest thing to do is to backup BLOSUM62, then save your test matrix with that name. Sneaky, but I think it will work.
<br><br>Marty<br><br><div><span class="gmail_quote">On 2/17/06, <b class="gmail_sendername">Theodore H. Smith</b> <<a href="mailto:email@example.com">firstname.lastname@example.org</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi people,<br><br>I'm just playing around with BLAST to see what it outputs. I figured<br>I'd better understand BLAST now as I'm going to have to understand it<br>by the end of this project anyhow. (I'm at the beginning of this
<br>project).<br><br>I'm trying to test a made up scoring matrix. It's a very simple one.<br><br># Here is a matrix I made up.<br> A R N D ...<br>A 1 -1 -1 -1<br>R -1 1 -1 -1<br>N -1 -1 1 -1<br>D -1 -1 -1 1<br>
...<br><br>This is just to get a better idea of how does BLAST work. However, I<br>can't figure out how to tell blast to use this matrix file! I don't<br>see it in the documentation, although I might have missed something.
<br><br>Any ideas anyone?<br><br>What this experiment is trying to figure out, is does BLAST return<br>multiple sections, when doing local alignments. Basically, the same<br>quesiton I have before about Smith-Waterman, I was trying to figure
<br>out how does BLAST work in the same respect. In other words, does<br>BLAST match BBBBAAAA to AAAABBBB, to give the alignments:<br><br>AAAA<br>::::<br>AAAA<br><br>and<br><br>BBBB<br>::::<br>BBBB<br><br>I thought I'd figure out the answer myself instead of asking, but I
<br>couldn't figure out how to input custom scoring matrixes :)<br><br>--<br><a href="http://elfdata.com/plugin/">http://elfdata.com/plugin/</a><br><br><br><br>_______________________________________________<br>Bioinformatics.Org
general forum - <a href="mailto:BiO_Bulletin_Board@bioinformatics.org">BiO_Bulletin_Board@bioinformatics.org</a><br><a href="https://bioinformatics.org/mailman/listinfo/bio_bulletin_board">https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
</a><br></blockquote></div><br><br clear="all"><br>-- <br>-- <br>Martin Gollery<br>Associate Director<br>Center For Bioinformatics<br>University of Nevada at Reno<br>Dept. of Biochemistry / MS330<br>775-784-7042<br>-----------