Ucsc Whole Genome Pairwise Alignment

Question

[masih.mahmoudi]

i need whole genome pairwise alignment between human and gorilla and chimp. I found the paiwise alignment file in UCSC genome browser http://hgdownload.soe.ucsc.edu/downloads.html

but i dont understand the structure of files there , they are some numbers without any nucleotide or usual alignment structure there, structure like this:

in the net file: fill 1395 20015 chrUn + 1855136 20062 id 2914 scor 1590070 ali 19664 qDup 19767 type top tN 0 qN 176 tR 14871 qR 14596 tTrf 287 qTrf 356 gap 3541 1 chrUn + 1855482 0 tN 0 qN 0 tR 1 qR 0 tTrf 0 qTrf 0

in the chain file:

chain 17470905528 chr1 249250621 + 87771 248804627 chr1 228333871 + 77636 228159347 1
15 1 0
6   1  0

what is the difference between net and chain files? i appreciate if anybody could help me how i can analyze these files?

[microfuge]

Hi, I liked the descriptions here - http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto http://genomewiki.ucsc.edu/index.php/Chains_Nets

Answer 1

[Biomonika (Noolean)]

You should read description of the files on the download page. This would point you to the explanation of net and chain files.

chain: http://genome.ucsc.edu/goldenPath/help/chain.html

net: http://genome.ucsc.edu/goldenPath/help/net.html