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A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Protein sequence-similarity search acceleration using a heuristic algorithm with a sensitive matrix.

Kyungtaek Lim¹, Kazunori D Yamada^1,2, Martin C Frith^1,3

¹Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.

Journal of Structural and Functional Genomics

|January 14, 2017

Summary

This summary is machine-generated.

The MIQS substitution matrix enhances protein homology detection when used with the LAST search tool. This combination offers faster and more accurate protein sequence analysis for genomics research.

Keywords:

Alignment quality Amino acid substitution matrix Homology detection

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Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

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Published on: August 16, 2017

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Protein database searching is crucial for structural and functional genomics.
Amino acid substitution matrices significantly impact homology detection accuracy.
Previous work introduced the MIQS matrix for distant protein homology search.

Purpose of the Study:

To evaluate the MIQS substitution matrix combined with the LAST sequence alignment tool.
To assess the performance of MIQS-LAST across various sensitivity parameters.
To compare MIQS-LAST against existing homology search methods.

Main Methods:

Utilized the MIQS substitution matrix with the LAST heuristic search tool.
Tested LAST with a tunable sensitivity parameter (m) on a large protein database (approx. 15 million sequences).
Compared performance against BLASTP, CS-BLAST, and SSEARCH.

Main Results:

MIQS significantly improved LAST's homology detection and alignment quality.
LAST with m=10^5 outperformed BLASTP and was 20x faster.
LAST with MIQS and m=10^6 showed comparable sensitivity to CS-BLAST and SSEARCH at higher speeds.

Conclusions:

MIQS-powered LAST provides a time-efficient method for sensitive and accurate protein homology searching.
This approach enhances target selection in structural and functional genomics.
The findings support the utility of MIQS for improving protein sequence analysis.