Can I run a blast for each contig in my contigs file?

Question

[roberto.bonnellya]

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.

[GenoMax]

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.html

Note: blat is free only for academic use.

Answer 1

[Darked89]

You can just use two fasta files:

• contigs.fa (to be converted to blast database)
• putative_genes.fa (to be searched against the first one.

No need to search all against all one by one.