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A workbench for large-scale sequence homology analysis

E L Sonnhammer¹, R Durbin

¹Sanger Centre, Hinxton Hall, Cambridge, UK.

Computer Applications in the Biosciences : CABIOS

|June 1, 1994

Summary

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Analyzing long DNA sequences is time-consuming. New tools, MSPcrunch and Blixem, improve the sensitivity and efficiency of BLAST searches, aiding in the discovery of distant protein similarities in genome projects.

Area of Science:

Bioinformatics
Genomics
Computational Biology

Background:

Genome sequencing projects generate vast amounts of DNA sequence data.
Analyzing database search results for protein similarities is often time-consuming and may miss distant evolutionary relationships.

Purpose of the Study:

To develop computational tools to streamline the analysis of large-scale DNA sequence data.
To enhance the sensitivity and efficiency of similarity searches in genomic databases.

Main Methods:

Development of MSPcrunch software to filter BLAST search results, removing biased and redundant matches while retaining significant weak matches.
Development of Blixem, an X-windows multiple sequence alignment viewer for visualizing and evaluating MSPcrunch-processed BLAST results.
Application of MSPcrunch and Blixem to analyze 1.2 megabases of C. elegans cosmid clone sequences.

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Main Results:

MSPcrunch improves BLAST search sensitivity, reducing the risk of overlooking distant similarities.
Blixem facilitates efficient scanning and evaluation of multiple sequence alignments in three reading frames.
The tools were successfully applied to a large dataset of C. elegans genomic sequences.

Conclusions:

MSPcrunch and Blixem significantly reduce the time and effort required for analyzing large DNA sequence datasets.
These tools enhance the ability to detect distant protein similarities, improving genomic analysis.
The developed software provides practical solutions for routine analysis in large-scale genome sequencing projects.