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Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction

Batzoglou, Serafim and Pachter, Lior and Mesirov, Jill P. and Berger, Bonnie and Lander, Eric S. (2000) Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction. Genome Research, 10 (7). pp. 950-958. ISSN 1088-9051. PMCID PMC310911. https://resolver.caltech.edu/CaltechAUTHORS:20170309-110441139

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Abstract

We describe a novel analytical approach to gene recognition based on cross-species comparison. We first undertook a comparison of orthologous genomic loci from human and mouse, studying the extent of similarity in the number, size and sequence of exons and introns. We then developed an approach for recognizing genes within such orthologous regions by first aligning the regions using an iterative global alignment system and then identifying genes based on conservation of exonic features at aligned positions in both species. The alignment and gene recognition are performed by new programs calledGLASS and ROSETTA, respectively.ROSETTA performed well at exact identification of coding exons in 117 orthologous pairs tested.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1101/gr.10.7.950DOIArticle
http://genome.cshlp.org/content/10/7/950.abstractPublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC310911/PubMed CentralArticle
ORCID:
AuthorORCID
Pachter, Lior0000-0002-9164-6231
Lander, Eric S.0000-0003-2662-4631
Additional Information:© 2000 Cold Spring Harbor Laboratory Press. The Authors acknowledge that six months after the full-issue publication date, the Article will be distributed under a Creative Commons CC-BY-NC License (Attribution-NonCommercial 4.0 International License, http://creativecommons.org/licenses/by-nc/4.0/). Received February 15, 2000. Accepted May 2, 2000. S.B., B.B., and this work were supported in part by Merck. L.P. was supported in part by a graduate fellowship from the Program in Mathematics and Molecular Biology and by a National Institutes of Health training grant. E.S.L. and J.M. were supported in part by a grant from the National Human Genome Research Institute. We thank Bruce Birren, Ken Dewar, and Daniel Kleitman for helpful discussions. We thank Eric Banks for support with software development. S.B. and L.P. contributed equally to this work. The publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked “advertisement” in accordance with 18 USC section 1734 solely to indicate this fact.
Funders:
Funding AgencyGrant Number
NIH Predoctoral FellowshipUNSPECIFIED
National Human Genome Research InstituteUNSPECIFIED
Issue or Number:7
PubMed Central ID:PMC310911
Record Number:CaltechAUTHORS:20170309-110441139
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170309-110441139
Official Citation:Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction Serafim Batzoglou, Lior Pachter, Jill P. Mesirov, Bonnie Berger, and Eric S. Lander Genome Res. July 1, 2000 10: 950-958; doi:10.1101/gr.10.7.950
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74978
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:10 Mar 2017 03:44
Last Modified:09 Mar 2020 13:18

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