BLAST one sequence set against another set of sequences. Each sequence of the query set is blasted against the other set and the best hit is returned. If no hit can be found for a query sequence null is returned. Additionally you can specify all BLAST parameters.

Needs formatdb and blastall installed on your machine and in the path!

Note: The identifiers of the sequences you are blasting against must be in the FASTA Defline format. Otherwise the identifier if your subject hits look like _1/$TMPDIR/DBXXX where the first number ist the index in the database sequence set starting with number 1.
Samples of correctly formatted identifier lines are:
 GenBank                           gi|gi-number|gb|accession|locus
 EMBL Data Library                 gi|gi-number|emb|accession|locus
 DDBJ, DNA Database of Japan       gi|gi-number|dbj|accession|locus
 NBRF PIR                          pir||entry
 Protein Research Foundation       prf||name
 SWISS-PROT                        sp|accession|name
 Brookhaven Protein Data Bank (1)  pdb|entry|chain
 Brookhaven Protein Data Bank (2)  entry:chain|PDBID|CHAIN|SEQUENCE
 Patents                           pat|country|number 
 GenInfo Backbone Id               bbs|number 
 General database identifier       gnl|database|identifier
 NCBI Reference Sequence           ref|accession|locus
 Local Sequence identifier         lcl|identifier