Hi everybody. I am using blast standalone 2.2.28+ in westgrid with linux for comparing two sequences (one short) and I do my best to use the same settings as blast website so:
blastn -query Spacers.HTBN.txt -db human.gut.fasta -gapopen 2 -gapextend 1 -penalty -3 -reward 1 -dust no -evalue 10 -word_size 10
but the results I get from the website VS linux have different e-values?! what can be the reason? i do really appreciate your help.