Dear all,
I want to compare a number of sequences with another list of sequences. Each comparison is consisted of only two sequences. I make an example below.
FILE1
>gene1_species1
atgcatgc>gene2_species1
tgcagcat
.........FILE2
>gene1_species2
atgGatgc>gene2_species2
tgcCgcGt
...........I need to compare gene1 and gene2 between these two species. One foolish way is to merge FILE1 and FILE2, and then blast itself (this is what I can think and do). My bigger problem is: I need to output the sequence alignment for each gene (please see below), rather than tabular blast result (-m 8 option). How to achieve this analysis? Would you please give me some suggestions? THANK YOU VERY MUCH!
gene1_species1 atgcatgc
gene1_species2 atgGatgc
gene2_species1 tgcagcat
gene2_species2 tgcCgcGt