Table 4.3Software tools for homology-based gene prediction

Program Authors, WWW site Comment Refs.
INFOMichael Laub http://elcapitan​.ucsd.edu/~info Compares the given DNA sequence against GenBank[492]
ORFGeneRogozin and Milanesi http://www​.itba.mi.cnr.it/webgene/ Compares translated DNA against SWISS-PROT[569]
PipMakerWebb Miller http://bio​.cse.psu.edu Aligns similar regions in two DNA sequences[759]
AATXiaoqiu Huang http://genome​.cs.mtu.edu/aat.html Searches the given DNA sequence against dbEST or HGI, or a protein against NR or SWISS-PROT[361]
ProcrustesA. Mironov, M. Gelfand, P. Pevzner, http://www-hto​.usc.edu​/software/procrustes Explores all possible exon assemblies in the given DNA sequence and finds the multi-exon structure with the best fit to a homologous protein[276]
GeneWiseEwan Birney, Richard Durbin http://www​.sanger.ac.uk/Software/Wise2 Compares a given protein sequence to a genomic DNA sequence, allowing for introns and frameshift errors[93]

From: Chapter 4, Principles and Methods of Sequence Analysis

Cover of Sequence - Evolution - Function
Sequence - Evolution - Function: Computational Approaches in Comparative Genomics.
Koonin EV, Galperin MY.
Boston: Kluwer Academic; 2003.
Copyright © 2003, Kluwer Academic.

NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.