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.
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KCC
Some binaries hanling the MAF files are available under http://hgdownload.cse.ucsc.edu/admin/exe/
for example mafsInRegion
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======== mafsInRegion ====================================
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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
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Pierre Lindenbaum
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.
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
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
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Casey Bergman
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/
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