Pairwise alignment for multiple sequences in two fasta files

Question

[nessrineN]

Hello,

I need some help for an assignment.Well I need to compare 135 human ATP binding site sequences with 7 plasmodium ATP binding site sequencies.These sequences are in two fasta file ( one for human sequence , one for plasmodium sequence). I have to find the 10 human ATP binding sequences that are the closest to the 7 plasmodium ATP binding site. For that I need to do a python code that is going to open my two fasta files then, compare each human sequence with the 7 plasmodium sequences and at the end , return to me the 10 closest human sequences.

To be honest I don't know what to do at all .

Thanks for your help :)

[Pierre Lindenbaum]

pairwise alignment for multiple sequences in a file

[lieven.sterck]

Does it have to be via python (guess so given it's an assignment)

otherwise you simply blast both fasta files to each other and parse the resulting output to find the most similar matches.

For a truly accurate selection of the closest one, you'd be better of building a (simple) phylogenetic tree with those sequences and then base your selection on the tree topology