Is There An Easy Way To Read The Maf Files On The Ucsc Website?

Question

[KCC]

MAF files are files which store multiple alignments. This is the format found on the UCSC Sequence and Annotation download page.

What kinds of software can I use to search these .maf files. I want to input the chromosome and position of a reference species and find the aligned sequences from the other species in the alignment. Ultimately, I want to see if a particular motif is preserved between species.

Answer 1

[Pierre Lindenbaum]

Some binaries hanling the MAF files are available under http://hgdownload.cse.ucsc.edu/admin/exe/

for example mafsInRegion

================================================================
========   mafsInRegion   ====================================
================================================================
mafsInRegion - Extract MAFS in a genomic region
usage:
    mafsInRegion regions.bed out.maf|outDir in.maf(s)
options:
    -outDir - output separate files named by bed name field to outDir
    -keepInitialGaps - keep alignment columns at the beginning and of a block that are gapped in all species

Answer 2

[Eric Fournier]

The Galaxy tools mentionned by Casey use bx-python internally, so you may want to use that if you'd rather work from a command line.

There is also a branch of Biopython with MAF handling tools.

[Thomas]

Hello, I know you posted your comment quite a while ago - but I found it useful in my own research.

I have installed the bx-python library on my local system - however I can't easily discern the relationship between the various python scripts in the library and the tools contained within the Galaxy platform.

In particular, I am interested in the 'Stich MAF blocks' function

I am not sure how I can use bx-python to implement this function locally without using Galaxy

Answer 3

[Casey Bergman]

There are also MAF extraction and conversion tools in Galaxy under the "Fetch Alignments" header. The tools you are probably looking for are "Extract Pairwise MAF blocks given a set of genomic intervals" and "Extract MAF blocks given a set of genomic intervals". See also: http://wiki.g2.bx.psu.edu/Main/MAF%20Analysis

Answer 4

[Gireesh K. Bogu]

You can download them from ucsc. For ex: hg19 MAF files in 46 vertebrates http://hgdownload.cse.ucsc.edu/goldenPath/hg19/multiz46way/maf/ . For aligning you can stitchedMAFblocks function in Galaxy or you can use MAF-Utilities under PHAST http://compgen.bscb.cornell.edu/phast/