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require('SSI_GDBprep.php');
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<h1 align=center><FONT color=#336666>Gene structure prediction from consensus spliced
alignment of multiple ESTs matching the same genomic locus</FONT></h1>
<p align=center>Volker Brendel, Liqun Xing, and Wei Zhu (2004) <I>Bioinformatics</I>
<B>20</B>, 1157-1169</p>
<P align='left'>
The GeneSeqer spliced alignment method is particularly suitable to applications when multiple
ESTs from heterogeneous sources match a given genomic locus.
By combining species-specific splice site prediction with sequence matching, the algorithm
can often successfully use non-cognate ESTs to derive accurate gene structure annotations.
The accuracy of prediction can be independently supported by the identification of long open
reading frames spanning the predicted exons.
Similarity of the predicted translation product to known proteins (and spliced alignment of
those proteins back onto the genomic locus) will in many cases provide complete annotation.
<P align='left'>
The cited paper describes the method in detail.
This site provides Supplementary Information, illustrating the method with typical examples.
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<h2><FONT color=#339999>Data Sets and Methods</FONT></h2>
<p>The basic algorithm implemented in GeneSeqer is described in
<A HREF="http://gremlin1.zool.iastate.edu/~volker/research/Bioinformatics16-203.pdf">Usuka, J., Zhu, W. & Brendel, V. (2000) Bioinformatics 16, 2003-211</A>
and
<A HREF="http://gremlin1.zool.iastate.edu/~volker/research/JMB297-1075.pdf">Usuka, J. & Brendel, V. (2000) J. Mol. Biol. 297, 1075-1085</A>.
The submitted manuscript describes recent developments concerning consensus (alternative)
gene structure predictions from multiple, overlapping spliced alignments.
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<h3><a href="AraSet/AraSet-AtGDB.php">AraSet</a></h3>
To benchmark the prospects and limits of gene prediction by spliced alignment, we
evaluated the GeneSeqer performance on the <a href="http://sphinx.rug.ac.be:8080/biocomp/GeneComp/">AraSet</a>
<I>Arabidopsis thaliana</I> gene set distributed for program testing purposes by
Pavy et al. (1999) Bioinformatics 15, 887-899.
This set consists of 74 contigs comprising two to four genes each, 168 genes and 859
introns in total.
Our spliced alignment results show that some of the AraSet annotation is incomplete
and incorrect currently.
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<h2><FONT color=#339999>Applications</FONT></h2>
The following links document particular results discussed in the submitted manuscript.
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<h3><a href="atac/gs_sorted-output-Ex1_top.html">Example of rice gene annotation with barley ESTs</a></h3>
This example shows how GeneSeqer can use ESTs from related species to predict gene structure
in a different species.
The particular gene analyzed contains a U12-intron with AT-AC borders which is correctly annotated by the GeneSeqer output.
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<h3><a href="OsBAC/gs_sorted-output-Ex2_top.html">Example of rice BAC annotation</a></h3>
To demonstrate the utility of GeneSeqer for large-scale (plant) genome annotation, we show analysis of a randomly selected rice BAC sequence.
Several gene structures are fully supported by EST evidence when ESTs from other plant species in addition to rice are used in the spliced alignment.
Correctness of the predictions is confirmed by similarity of the predicted gene products to other proteins.
All analysis can easily be reproduced using the <A HREF="http://www.plantgdb.org/cgi-bin/GeneSeqer.cgi">GeneSeqer Server at PlantGDB</A>.
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