Question: Extract alignment blocks of a given region from MAF file having whole genome alignments
0
gravatar for urjaswita
2.5 years ago by
urjaswita90
United States
urjaswita90 wrote:

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.

ADD COMMENTlink modified 6 months ago by Zhenpeng Yu0 • written 2.5 years ago by urjaswita90

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.

ADD REPLYlink written 2.5 years ago by Joe16k
1
gravatar for Emily_Ensembl
2.5 years ago by
Emily_Ensembl20k
EMBL-EBI
Emily_Ensembl20k wrote:

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

ADD COMMENTlink written 2.5 years ago by Emily_Ensembl20k
0
gravatar for Zhenpeng Yu
6 months ago by
China/Nanjing/Nanjing Normal University
Zhenpeng Yu0 wrote:

I think the software maffilter will be useful for you.

https://github.com/jydu/maffilter

ADD COMMENTlink modified 6 months ago • written 6 months ago by Zhenpeng Yu0
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