Align against reference genome and extract selected regions

I would like to extract selected genomic region containing a protein we are studying and 1-2 Kb up- and down-stream.

I thought performing alignment against reference genome and parsing the MAF file would be feasible.

Could you suggest me some tools to perform this task?

Thanks!

parse

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written 11.5 years ago by biotech

I'm also considering some alternatives to perform this task, such as BLASTn Extract fasta from BLAST hits

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written 11.5 years ago by biotech

What exactly are you trying to align against the genome? A single sequence, a large dataset, something else entirely?

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written 11.5 years ago by Devon Ryan

200 bacterial draft genomes of the same specie.

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written 11.5 years ago by biotech

1 answer

200 bacterial genomes.

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written 11.5 years ago by biotech

Please admin, could you delete this answer? I can't find how.

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written 11.5 years ago by biotech

FYI, I deleted that answer for you.

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written 11.5 years ago by Devon Ryan

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