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<DIV><SPAN class=933120815-18112005><FONT face=Arial color=#0000ff
size=2>Alternatively, you can use Splign or Spidey from
NCBI...</FONT></SPAN></DIV>
<DIV><SPAN class=933120815-18112005></SPAN> </DIV>
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<DIV></DIV>
<DIV class=OutlookMessageHeader lang=en-us dir=ltr align=left><FONT
face=Tahoma size=2>-----Original Message-----<BR><B>From:</B>
bio_bulletin_board-bounces+golharam=umdnj.edu@bioinformatics.org
[mailto:bio_bulletin_board-bounces+golharam=umdnj.edu@bioinformatics.org]
<B>On Behalf Of </B>Stefanie Lager<BR><B>Sent:</B> Friday, November 18, 2005
3:31 AM<BR><B>To:</B> Evgeny Cheremushkin; The general forum at
Bioinformatics.Org<BR><B>Subject:</B> Re: [BiO BB] How to align whole query
sequence with blast<BR><BR></FONT></DIV>
<DIV>If you want to align cDNA or proten sequences to genomic DNA it's better
to use the algorithms GMAP <A
href="http://www.gene.com/share/gmap">http://www.gene.com/share/gmap</A>
or Exonerate <A
href="http://www.ebi.ac.uk/~guy/exonerate/">http://www.ebi.ac.uk/~guy/exonerate/</A> instead
of BLAST . These two algorithms are faster then blast, and they are made to
handle introns.</DIV>
<DIV> </DIV>
<DIV>Wu TD, Watanabe CK. <BR>GMAP: a genomic mapping and alignment program for
mRNA and EST sequences.<BR>Bioinformatics. 2005 May 1;21(9):1859-75. Epub 2005
Feb 22. <BR>PMID: 15728110 </DIV>
<DIV> </DIV>
<DIV>Slater GS, Birney E. <BR>Automated generation of heuristics for
biological sequence comparison.<BR>BMC Bioinformatics. 2005 Feb 15;6(1):31.
<BR>PMID: 15713233</DIV>
<DIV> </DIV>
<DIV>Stefanie<BR><BR> </DIV>
<DIV><SPAN class=gmail_quote>On 11/18/05, <B class=gmail_sendername>Evgeny
Cheremushkin</B> <<A
href="mailto:cher@biorainbow.com">cher@biorainbow.com</A>> wrote:</SPAN>
<BLOCKQUOTE class=gmail_quote
style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hello
bio_bb,<BR><BR>I want to align whole query sequence onto genome
with blast<BR>(not only a part of query sequence). Is there any option for
<BR>that?<BR><BR>--<BR>Best regards,<BR>Evgeny Cheremushkin,<BR>BioRainbow
Group,<BR>phone: +7 (383) 3306470<BR>mobile: +7 (913)
8916858<BR>e-mail: <A
href="mailto:cher@biorainbow.com">cher@biorainbow.com</A><BR>web: <A
href="http://www.biorainbow.com">http://www.biorainbow.com</A><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></BLOCKQUOTE></BODY></HTML>