Blast

Blast alignment algorithm

Here's a very useful looking page that explains how the blast algorithm parameters work @http://www.clcbio.com/index.php?id=995

example blast command blasting two fasta files against eachother (executed from C:\kurt\storage\CIM Research Folder\DR\2013\3-30-13\sequence analysis) blastp -task blastp-short -db prot_3-30-13.fa -query "C:\kurt\storage\CIM Research Folder\DR\2013\3-25-13\her2 peptides\all peptides without CSG.fa" -out results_3-30-13_1747.txt

Make a BLAST database 3-30-13