The MIT LCS Computation and Biology group and the MIT Center for Genome Research support two experimental tools for cross-species comparative analysis and gene recognition:


GLASS (GLobal Alignment SyStem) is a tool for aligning pairs of homologous sequences. It is designed for aligning long, divergent sequences, that contain blocks of moderate to strong homology, such as orthologous/paralogous pairs of genes.

Submit online GLASS queries.

Download the current GLASS source code.


Rosetta is a tool for predicting coding exons on a target human sequence (may also work for other mammalian sequences as targets), based on comparison with a homologous sequence from a different species.

We are currently updating Rosetta, please check back soon!

GLASS and Rosetta are both described in:

S. Batzoglou, L. Pachter, J.P. Mesirov, B. Berger, and E.S. Lander. "Human and mouse Gene Structure: Comparative Analysis and Application to Exon Prediction." Genome Research, July 1, 2000. Abstract in RECOMB 2000, Tokyo, April 2000.

The following files are provided here as supplimentary material to the above publication:

Table of Comparative Analysis of 117 Orthologous Human and Mouse Loci

GenBank Records of the 117 Orthologous Human and Mouse Loci Analyzed

For further information about GLASS and Rosetta, please contact: