The Gene2EST Server

gibson gibson at embl-heidelberg.de
Wed Oct 18 10:45:37 EST 2000


This note is to announce a new BLAST2 server specialised for querying
EST databases with eukaryotic gene-sized queries, which may often be in,
say, the 50-100 KB range. This server maps ESTs onto the query - it
should not be confused with gene prediction algorithms. Gene2EST is
primarily targeted to help the researcher who wishes to examine a few
genes in high detail and is not suitable for high throughput analyses.

The server is at http://woody.embl-heidelberg.de/gene2est/

Gene2EST uses RepeatMasker
(http://ftp.genome.washington.edu/RM/RepeatMasker.html) and Repbase to
filter out dispersed repetitive sequences (Alus etc.) from the query.
(Since many of these are expressed and are therefore abundant in EST
DBs, it is well known that they often confound gene-based queries.)

As well as allowing large queries, useful Gene2EST features include two
novel output files parsed from the BLAST output:

1. A multiple alignment of all EST HSPs on the query sequence.
2. An EMBL format file in which the ESTs are represented as mRNA
features. This output is for display in a graphical display tool such as
Artemis4 (freely available for all platforms from
http://www.sanger.ac.uk/Software/Artemis/v4/). In favourable cases (i.e.
lots of ESTs), this display can reveal the entire gene structure,
including alternative splicing.

Please note that, depending on query size and number of EST matches,
Gene2EST outputs can be rather large files. This could cause problems
for some users e.g. using old desktop machines with limited memory, or
with slow internet links.

Gene2EST is a new server and may not be completely robust: Please report
any problems to us.  Suggestions are also welcome.

Toby Gibson, Christine Gemuend, Ramu Chenna and Brigitte Altenberg








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