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Question: Stitch MAF blocks
0
gravatar for kasthuri
4.6 years ago by
kasthuri • 0
United States
kasthuri • 0 wrote:

This is about the module "Stitch MAF blocks" which can be found in "Fetch Alignments" in Galaxy.

Can somebody explain how Galaxy "stitches" different sequences from different species based on a given sequence in a species? How does it know the coordinates in other species or does it simply blasts the sequence against other genomes?

Thanks
fetch alignments stitch maf species • 1.3k views
ADD COMMENT • link •
modified 4.6 years ago by Daniel Blankenberg ♦♦ 1.7k • written 4.6 years ago by kasthuri • 0
1
gravatar for Daniel Blankenberg
4.6 years ago by
Daniel Blankenberg ♦♦ 1.7k
United States
Daniel Blankenberg ♦♦ 1.7k wrote:

This tool simply uses the regions provided by the user, which belong to a specific genome build, and uses the aligning columns/bases in the other genome builds and stitches the individual sequences together.
ADD COMMENT • link written 4.6 years ago by Daniel Blankenberg ♦♦ 1.7k

Thank you Daniel. I realize this, but how does a region belonging to a  specific genome build align to other genome builds? I mean do you blast the given sequence (in the specific genome build) against other genomes fasta and pick those sequences that are highly similar? Is it a homology based mapping?

Thanks again.

ADD REPLY • link written 4.6 years ago by kasthuri • 0
2

You are using 2 sets of data here, a set of genomic intervals/regions/coordinates and a set of precomputed alignments (MAF: http://genome.ucsc.edu/FAQ/FAQformat.html#format5). You always provide the genomic intervals, but you either provide your own MAF file via your history or you select from a list of built-in/precached MAFs. Most of the alignments that we provide are created by the UCSC pipeline using multiZ, for example, you can learn more about the 100way alignment from their download page, here: http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/multiz100way/

Hope that helps.

ADD REPLY • link written 4.6 years ago by Daniel Blankenberg ♦♦ 1.7k

Thank you Daniel. This helps. I have been using built-in MAFs. And I see they are created by multiZ. This is good to know.

K.

ADD REPLY • link written 4.6 years ago by kasthuri • 0
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