blast query using list instead of single .fa files from command line?

Question

[goatsrunfaster]

I have a large number of short sequences I want to blast against each other. is there a way (other than setting up a single pairwise query for each), to use two lists to get pairwise comparisons for hundreds of .fa files? Any help is appreciated.

[lieven.sterck]

why don't you cat them in a single (big) file , created blast DB from it and then blast the file against the DB . Afterwards parse out all pairwise alignments.