Align two fasta files together, each with multiple sequences

Question

[msening]

Hi, I have two fasta files that I want to align together. One (A) contains fragments of a sequence that is created by a sliding window step size of 1. The other one (B) is multiple sequences. I want to align A with B and use the output (can I only get one output?) to label the fragment in A (to show that it was mapped to a sequence in B). I tried to use bowtie 2 but apparently, I have to use a fastq file. I also wanted to try emboss water but I am not sure if I can use it for multiple sequences for both files.

Is there anyway I can achieve this?

Answer 1

[GenoMax]

If the sequences are similar (and or a similar length) you could try Jim Kent's blat. It will take multiple sequences in both files and produce results for all comparisons by a single command line. You can easily parse tabular output should you choose to do do.

You can use -f option with bowtie2 to specify that input reads are fasta. You don't need to use fastq files. You can use it since you will be creating an index with one of the files (with multiple sequences) and then aligning the sequences to this index one at a time from query file.

[msening]

I decided to go with bowtie2 because I'm more familiar with bowtie in general. Thank you for the tip about using -f!