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A Practical Guide to Phylogenetics for Nonexperts

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Fast comparison of a DNA sequence with a protein sequence database

¹Department of Computer Science, Michigan Technological University, Houghton, USA.

Microbial & Comparative Genomics

|January 1, 1996

Summary

A new computer program, DNA-Protein Search (DPS), efficiently compares large DNA sequences to protein databases, identifying coding regions and outperforming BLASTX in speed and memory usage.

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Comparing large DNA sequences with protein databases is crucial for genomic analysis.
Existing tools like BLASTX face challenges with computational resources and speed when handling megabase-scale sequences.
Identifying coding regions within genomic DNA requires accurate and efficient sequence alignment methods.

Purpose of the Study:

To introduce and evaluate the DNA-Protein Search (DPS) program for comparing megabase DNA sequences against protein databases.
To address challenges posed by frameshifts and introns in DNA sequence analysis.
To assess the performance of DPS in terms of speed, memory usage, and sensitivity in identifying coding regions.

Main Methods:

Development of the DNA-Protein Search (DPS) computer program.

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Comparison of large DNA sequences (Haemophilus influenzae Rd, Mycoplasma genitalium, Saccharomyces cerevisiae chromosome VIII) with the Swiss-Prot protein database using DPS.

Evaluation of DPS sensitivity using known coding regions from the tested DNA sequences.

Benchmarking DPS against the BLASTX program for speed and computer memory efficiency.

Main Results:

DPS successfully identified novel regions of similarity between DNA sequences and known proteins.
The program effectively handled frameshifts and introns within the DNA sequences.
Sensitivity analysis confirmed DPS's capability in detecting known coding regions.
DPS demonstrated superior performance, using significantly less computer memory and operating several times faster than BLASTX.

Conclusions:

The DNA-Protein Search (DPS) program is a valuable and efficient tool for analyzing large-scale genomic data.
DPS offers a significant computational advantage over existing methods like BLASTX for DNA-protein sequence comparisons.
The program facilitates the discovery of coding regions and enhances genomic research capabilities.