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Open Access Highly Accessed Software

Reference based annotation with GeneMapper

Sourav Chatterji1* and Lior Pachter2

Author Affiliations

1 Department of Computer Science, University of California at Berkeley, Berkeley, CA, 94720, USA

2 Department of Mathematics, University of California at Berkeley, Berkeley, CA 94720, USA

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Genome Biology 2006, 7:R29  doi:10.1186/gb-2006-7-4-r29

Published: 5 April 2006

Abstract

We introduce GeneMapper, a program for transferring annotations from a well annotated genome to other genomes. Drawing on high quality curated annotations, GeneMapper enables rapid and accurate annotation of newly sequenced genomes and is suitable for both finished and draft genomes. GeneMapper uses a profile based approach for mapping genes into multiple species, improving upon the standard pairwise approach. GeneMapper is freely available for academic use.