FASTA Sliding 80mer Window 8mer Exact Match - HOW TO

Question

[maxpayneb13]

Hello, I don't know much about biology and dna and stuff... so forgive me if I say anything stupid :)

OK I'm trying to use fasta program + php to create a web based Protein Sequence Search for a friend

I don't have any problem in programing part and I could run a simple full query search using fasta35 program like this:

fasta35 -q -H -B -m 9i -w 80 -E 1 -d 20 /PATH/TO/temp_seq.aa /PATH/TO/lib.fasta

I found the above query on internet and it works.

My question is if I want to run an Sliding 80mer Window or 8mer Exact Match what options (args) should I pass to fasta program?

Answer 1

[Ram]

Hi,

I'd suggest using NCBI's standalone BLAST+ and if you need a web interface, to set up a standalone WWW BLAST server. This would help you leverage the power, modularity and flexibility of BLAST while enabling you to use it from anywhere and query against your custom databases.

I'd recommend trying to avoid reinventing the wheel in creating your own sequence alignment tools.