<DIV><BR>sir...plz tell me how to perform statistical evaluation of seq alignment and calculate Z-score</DIV>
<DIV>am a comp science student from india</DIV>
<DIV> thank you sir,</DIV>
<DIV> from</DIV>
<DIV> prathibha bharathi</DIV>
<DIV><BR><B><I>Renyi Liu <lry_biocomp@hotmail.com></I></B> wrote:</DIV>
<BLOCKQUOTE class=replbq style="BORDER-LEFT: #1010ff 2px solid; MARGIN-LEFT: 5px; PADDING-LEFT: 5px">Hi, Pankaj,<BR><BR>Since the number of sequences is not so big, I would use Smith-Waterman <BR>algorithm to obtain optimal local alignment between any two sequences.<BR><BR>For multiple alignment, I would try T_Coffee or/and Dialign2. Both program <BR>can be downloaded from the internet, but I am not sure if they can handle <BR>100 sequences.<BR><BR>Good luck,<BR><BR>Renyi<BR><BR><BR>>From: Pankaj <PANKAJ@NII.RES.IN><BR>>Reply-To: bio_bulletin_board@bioinformatics.org<BR>>To: bio_bulletin_board@bioinformatics.org<BR>>Subject: [BiO BB] alignment problem<BR>>Date: Wed, 21 Jan 2004 14:25:56 +0530 (IST)<BR>><BR>>hi all,<BR>>i have 100 sequences. i want to find the percentage simialrity of<BR>>every sequence to every other sequence. ie i want to prepare a 100X100<BR>>matrix. i m using local blast from ncbi to find the similarity. but<BR>>sometimes t
he
output file from blast has 2 alignments between the<BR>>sequences. ie sequence1 with sequence2 has 2 possible alignments (ie<BR>>over different parts of the sequences). how do i find the percentage<BR>>similarity between the sequences.<BR>>if i multipli align these 100 sequences by clustalw, i can see large<BR>>gaps in certain regions but i know that all these sequences catalyse<BR>>the same reaction.<BR>>thanks in advance<BR>>pankaj<BR>><BR>>_______________________________________________<BR>>BiO_Bulletin_Board maillist - BiO_Bulletin_Board@bioinformatics.org<BR>>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board<BR><BR>_________________________________________________________________<BR>Get a FREE online virus check for your PC here, from McAfee. <BR>http://clinic.mcafee.com/clinic/ibuy/campaign.asp?cid=3963<BR><BR>_______________________________________________<BR>BiO_Bulletin_Board maillist -
BiO_Bulletin_Board@bioinformatics.org<BR>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board</BLOCKQUOTE><p><font face=arial size=-1>
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