multiple sequences extraction from fasta

[sebl]

Hi,

I went through the forum but I couldn't find anything that does exactly what I need.

I would like to automatically search for multiple sequences (say, MLST loci) in a batch of genomes files in fasta format, then extract the results (the sequences) for further analysis. Say I want to search for a dozen loci in a list of genome files with a single command.

I guess there are scripts ready for the task, but I couldn't find.

Thanks a lot in advance!

[JackieBadger]

what do you mean by search?

You want to search based on sequence similarity to known genes or search based on a known sequence identifier?

[sebl]

I meant search by similarity, thank you.

[JackieBadger]

Without knowing how many sequences you want to compare, the obvious choice would be to use BLAST

[JohnN]

How big is the string that you want to look for? Gene-sized? Use BLAST. A few to a few dozen nucleotides, "grep" or a string search tool would work.

[GenoMax]

BLAT is also very useful (and quick) for such similarity searches.

[sebl]

I meant to search for gene sized sequences.

The question is if there is a script to allow automatic BLAST search of a list of sequence queries in a list of genome files, and returns the results (best only) so that I can more easily go on from there into further analysis.