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Bioinformatics Advance Access originally published online on February 12, 2004
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Bioinformatics 20(9) © Oxford University Press 2004; all rights reserved.

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, Maxim Shklar , Tsippi Iny Stein 2, Orit Shmueli 2, Marilyn Safran 1 and Doron Lancet 2,*

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

Received on July 12, 2003; revised on September 2, 2003; accepted on December 19, 2003
Advance Access Publication February 12, 2004

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 relationship 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 information: Program description and statistics http://genecards.weizmann.ac.il/geneannot/DOC/index.html

Contact: geneannot{at}weizmann.ac.il

* To whom correspondence should be addressed.


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