search fasta

[maria_mari]

Hi
I want a program/script to search a multifasta file like hg18.fa genome write the output as a bed file with coordinates. Does anybody know any script/package ..?

Thank you

[sphil]

Bed files indicate read coverage at a certain position of a genome. A fastA carries the genome itself. I doubt that there is such a script. For what purpose do you need it?

[GenoMax]

If I understand the question correctly then you could do a blat search against the genome file and then use the standard blat output (PSL format) to convert the relevant parts to a bed file.

A google search led me to this script (I have not tried it): http://davetang.org/wiki/tiki-index.php?page=Blat.