Searching for primers (and its rev compl.) in PACMAN

Question

[umn_bist]

Just curious if this is doable with a simple terminal command line.

I have a file of primers (each primer is /n - new line - delimited). I also have a text file (I guess, also fasta format is easily convertible) of the entire pacman (BAC) sequence.

I would like to feed my primer file and the reverse complement file to see if there is any matches in the BAC file. If there is, I would like to have it return which primer sequence matched.

Command line or a tool - I have no preference. Thank you very much!

[gangireddy]

Why don't you use blast or blat

Answer 1

[Biomonika (Noolean)]

Try primersearch from EBOSS.