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.
>gene1_species1 atgcatgc >gene2_species1 tgcagcat .........
>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