Extract alignment blocks of a given region from MAF file having whole genome alignments

Question

[urjaswita]

I am trying to extract blocks of alignments from Ensembl or UCSC whole genome alignment files in MAF format given an organism, chromosome and start-end position. For example, I want to extract the block from a maf file that encompass rat chromosome 1 from sequence position 236456 to 236723. And it should output the block alignment of this rat region with all the species that are aligned. Note please that my organism is not the reference organism in MAF and I have sequence positions.

Basically I have a bed file of some genomic regions in rat (sequence coordinates), and I want to extract the alignment that cover these regions in the maf files in other species.

I found a few utilities but couldn't get them working for my problem.

maf_parse in PHAST http://compgen.cshl.edu/phast/help-pages/maf_parse.txt

WGA_Bed https://github.com/henryjuho/maf_parse

Any help will be much appreciated. Thanks.

[Joe]

If you aren't wedded to MAF format, you can get FASTA alignments of large sequences from Kalign, and you may well find more tools to give you back 'slices' of sequence with a fasta than with MAF - I know I've struggled with MAF in the past.

Answer 1

[Emily]

There is an Ensembl REST API endpoint that gets you alignments for a given region, but won't give you MAF as an output.

Answer 2

[Zhenpeng Yu]

I think the software maffilter will be useful for you.

https://github.com/jydu/maffilter