Title: | Enumerating Alternative Spliced Transcripts for Understanding Complexity of the Human Genome |
Authors: | Shinichi Morishita, Jun Ogasawara, Toshihiko Honkura, and Tomoyuki Yamada |
Series: | Linköping Electronic Articles in Computer and Information Science ISSN 1401-9841 |
Issue: | Vol. 6 (2001): no 020 |
URL: | http://www.ep.liu.se/ea/cis/2001/020/ |
Abstract: |
According to recent several reports, the number of human genes is
estimated fewer than 40,000, which, surprisingly, is only double
the number (19,000) present in Caenorhabditis elegans.
This fact indicates that the correlation between complexity of
a species and its gene number appears to be loose, motivating studies on
other sources of complexity such as alternatively splicing and
cis-regulatory machinery.
The first step towards
this research direction would be to list candidates of alternatively
spliced transcripts and promoters.
Because of the release and updates of the human genome,
this enumeration could be achieved by aligning millions of expressed
sequence tags (ESTs, for short) to a draft human genome and then
organizing alignments into related groups,
which is however computationally costly.
We have developed an efficient algorithm for this purpose,
taking only one day to align three millions of ESTs to a newly revised draft
genome from scratch. Analysis of 2.2 millions of alignments identifies
about 8,000 groups of alternatively spliced transcripts.
A typical group contains tens of alignments, demanding a method of
selecting representatives.
All the results are accessible through the WWW
at our Gene Resource Locator web site
http://grl.gi.k.u-tokyo.ac.jp/
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Keywords: |
Original publication 2001-08-30 |
Postscript Checksum |
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