Multiple alignment for ChIP-seq data

Question

[tblain]

We are interested in looking at conservation using the Phast tool. Phast requires a .maf (multiple alignment format) file. Is anybody aware of a tool available to generate a .maf file from multiple ChIP-seq FASTQ files?

Answer 1

[Devon Ryan]

You don't need a dedicated tool for this. You have peaks in BED format, so use bedtools getfasta to get a multi-fasta file. Then use that in your multiple sequence alignment tool of choice. Note that you may need to reduce the number of regions, since most multiple sequence alignment programs would fail completely on ChIP-sized data.

BTW, you probably don't really want to do any of this. What I expect you're trying to do is to perform motif detection in your peaks. There are tools meant to do exactly that, such as MEME-ChIP.