Dear all,
I need to identify the homologs of many short sequences, and then make statistics of the mismatch and gap positions between each short sequence and its homolog. The first step can be readily done by BLAST, FASTA or patscan, but the second step is a little bit troublesome for me. I am wondering if it's feasible to parse the BLAST or FASTA result, and transform the alingment to mismatch and gap information using a perl script. Would you please suggest me some tools and methods to achieve this analysis? Is there a perl script to extract the information i need from BLAST/FASTA output?
Thank you very much!
I need to identify the homologs of many short sequences, and then make statistics of the mismatch and gap positions between each short sequence and its homolog. The first step can be readily done by BLAST, FASTA or patscan, but the second step is a little bit troublesome for me. I am wondering if it's feasible to parse the BLAST or FASTA result, and transform the alingment to mismatch and gap information using a perl script. Would you please suggest me some tools and methods to achieve this analysis? Is there a perl script to extract the information i need from BLAST/FASTA output?
Thank you very much!
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