[Genome] Multiz maf, ftp and intersection

[Brooke Rhead]

Hello Jimmie,

There is not a way to obtain sequence from our MySQL server, as the 
sequence is stored only in the MAF file, not in a table.

If you want to work with MAF files at the command line, there are some 
tools in the Genome Browser source tree for working with MAFs, 
(http://genomewiki.ucsc.edu/index.php/Kent_source_utilities -- search 
for "maf").  You can download the source from:
http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads
Run any command with no arguments to see a usage statement.  For example:

$ 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

Another option for working with MAFs is the Galaxy website, 
http://main.g2.bx.psu.edu/ .  Galaxy is run by Penn State but works in 
conjunction with the UCSC Genome Browser.  Look under the "Fetch 
Alignments" header on the left-hand side of the page for several tools 
for working with MAFs.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Ye, Jimmie wrote:
> Hi,
> 
> I'm interested in obtaining maf alignments in bulk but I need to be able
> to intersect the output of multiz17way with the list of known genes like
> the option that's available under the table browser...how can I do this
> in mysql?  Can someone from UCSC perhaps post a sample query in sql?
> 
> Thanks
> 
> ~Jimmie
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