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Compass of 47,787 cattle ESTs.

M Rebeiz¹, H A Lewin

¹Department of Animal Sciences, The W.M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, 61801, USA.

Animal Biotechnology

|August 23, 2000

Summary

A new computer program uses Comparative Mapping by Annotation and Sequence Similarity (COMPASS) to predict cattle expressed sequence tag (EST) locations. This tool helps map thousands of cattle ESTs by identifying human orthologs and their chromosome positions.

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Area of Science:

Genomics
Comparative Genomics
Bioinformatics

Background:

Comparative Mapping by Annotation and Sequence Similarity (COMPASS) is an established method for predicting the chromosomal locations of expressed sequence tags (ESTs).
Efficiently applying COMPASS to large datasets requires computational tools.

Purpose of the Study:

To develop and utilize a computer program for large-scale application of the COMPASS strategy.
To identify orthologs and predict map locations for a substantial number of cattle ESTs.

Main Methods:

Development of a computational tool to automate the COMPASS strategy.
Analysis of 47,787 cattle ESTs against the human UniGene database.
Annotation of cattle ESTs using human GB4 radiation hybrid mapping data.

Main Results:

The program successfully predicted map locations for 47,787 cattle ESTs.
30,097 cattle ESTs showed significant matches with human UniGene sequences.
21,311 cattle ESTs were annotated with human GB4 mapping data, providing putative human orthologs and predicted cattle chromosome locations.

Conclusions:

The developed program effectively executes the COMPASS strategy on a large scale.
The identified orthologs and predicted locations serve as a valuable resource for cattle genomics research.
This study facilitates a deeper understanding of cattle genome organization through comparative mapping.

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