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Bioinformatics Advance Access published online on February 12, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth081
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received July 12, 2003
Revised September 2, 2003
Accepted December 19, 2003

Applications note

GeneAnnot: comprehensive two-way linking between oligonucleotide array probesets and GeneCards genes

Vered Chalifa-Caspi 1*, Itai Yanai 2, Ron Ophir 1, Naomi Rosen 2, Michael Shmoish 2, Hila Benjamin-Rodrig 3, Tsippi Iny Stein 2, Orit Shmueli 2, Marilyn Safran 1, Doron Lancet 2

1 Department of Biological Services, the Weizmann Institute of Science, 76100 Rehovot, Israel
2 Department of Molecular Genetics, the Weizmann Institute of Science, 76100 Rehovot, Israel
3 Department of Physics of Complex Systems, the Weizmann Institute of Science, 76100 Rehovot, Israel

* To whom correspondence should be addressed. E-mail: bgumail.bgu.ac.il.


  Abstract

Motivation: High density oligonucleotide arrays are usually annotated in a one-to-one fashion, with each probeset assigned to one gene. However, in reality, subsets of oligonucleotides in a probeset may match sequences within more than one gene, potentially leading to misinterpretations. Moreover, a gene is often represented by more than one probeset, and analyzing probe matches at the mRNA level can help one deduce whether these probesets are derived from the same or different splice variants.

Results: The GeneAnnot system comprehensively documents the many-to-many relationships between oligonucleotide array probesets and annotated genes in GeneCardsTM. It performs pairwise alignments between the probe sequences and gene transcripts, and assigns sensitivity and specificity scores to each probeset/gene pair.

Availability: http://genecards.weizmann.ac.il/geneannot

Supplementary material: GeneAnnot program description and statistics http://genecards.weizmann.ac.il/geneannot/DOC/index.html.


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