Hi! You can change Blast output to XML. Use option '-m 7' for NCBI Blast. Greetings, Wolfgang Strasser ________________________________ Von: biodevelopers-bounces+wolfgang.strasser=fh-hagenberg.at at bioinformatics.o rg [mailto:biodevelopers-bounces+wolfgang.strasser=fh-hagenberg.at at bioinfor matics.org] Im Auftrag von Prabu R Gesendet: Donnerstag, 20. Juli 2006 18:01 An: Programming for bioinformatics Betreff: [Biodevelopers] Blast Output Parsing Dear All! I am now trying to parse a Blast output using PERL. I have to extract each alignment and have to parse the alignment. I mean, I have to check whether a particular part of the given sequence got aligned 100%. Anybody please tell me what module in PERL I have to use for getting this. I've tried Bio::SearchIO. But I didnt get any method to get the alignment. Kindly help. Thanks, R. Prabu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://bioinformatics.org/pipermail/biodevelopers/attachments/20060721/51c87a42/attachment.html