Can I run a blast for each contig in my contigs file?
Hello,
I want to do local alignment with the sequence of a gene against each contig in a contigs file. I wanted to know if there was any program to do this automatically, as my file has 400+ contigs.
Thanks for reading.
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roberto.bonnellya •
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roberto.bonnellya •
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If your sequence is homologous you can use
blat. One file (gene) against the other (contigs, database). No need to create indexes etc. More info here: https://genome.ucsc.edu/goldenpath/help/blatSpec.htmlNote:
blatis free only for academic use.