Che, Anney (NIH/NIAID) wrote: > Does anyone know how to set a filter in blast to omitting the replicated > hits? > > Thanks, Anney Hope this helps. I keep a text 'gilist.txt' file with this format: GI#1 <tab> a description of the sequence GI#2 <tab> a description of the sequence GI#3 <tab> a description of the sequence When I want a filter that will only see 'mouse' sequences. I run this command: grep mouse gilist.txt | cut -f 1 > filter.txt Then you run blast as you normally would but with an extra -l switch. blastall -p blastn -d database -i query -l filter.txt Optionally. If you'll be using the filter several times you may want to make a binary version which will allow blast to run faster. You can use this file in place of 'filter.txt' for a quite a little boost of extra speed. formatdb -F filter.txt -B filter.bin followed by blastall -p blastn -d database -i query -l filter.bin Since this is bioclusters, I'll mention that this also works very well with mpiblast. Michael Cariaso Bioinformatics Developer Besthesda, MD cariaso at yahoo dot com