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ABCC Applications Web Page
Welcome to the ABCC Accessible Application Web Page.
From this page, you can get information about our scientific applications and databases. To get more information about any topic, or to run an application, click on any of the mouseover popup menu items on the left-hand side. Program with a tag "Run" is runnable. This site continues to grow, so come back often to check out the many accessible applications available here at the Advanced Biomedical Computing Center (ABCC).
If you have any comments or suggestions, please contact us Help link
Blat Server
Blat
BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 40 bases or more.
It may miss more divergent or shorter sequence alignments. It will find perfect sequence matches of 33 bases,
and sometimes find them down to 22 bases. BLAT on proteins finds sequences of 80% and greater similarity of
length 20 amino acids or more.
In practice DNA BLAT works well on primates, and protein blat on land vertebrates
BLAT is not BLAST. DNA BLAT works by keeping an index of the entire genome in memory.
The index consists of all non-overlapping 11-mers except for those heavily involved in repeats.
The index takes up a bit less than a gigabyte of RAM. The genome itself is not kept in memory,
allowing BLAT to deliver high performance on a reasonably priced Linux box.
The index is used to find areas of probable homology, which are then loaded into memory for a detailed alignment.
Protein BLAT works in a similar manner, except with 4-mers rather than 11-mers. The protein index takes a little
more than 2 gigabytes
Website: Click Here
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