Align against reference genome and extract selected regions

Question

[biotech]

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!

[biotech]

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

[Devon Ryan]

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

[biotech]

200 bacterial draft genomes of the same specie.