ArticleBioinformatics (Oxford, England)2014
Revisiting amino acid substitution matrices for identifying distantly related proteins.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30 citing papers in PubMed.
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- Proteome-Wide Structural Computations Provide Insights into Empirical Amino Acid Substitution Matrices.International journal of molecular sciences · 2023Article
- New alignment method for remote protein sequences by the direct use of pairwise sequence correlations and substitutions.Frontiers in bioinformatics · 2023Article
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- Snekmer: a scalable pipeline for protein sequence fingerprinting based on amino acid recoding.Bioinformatics advances · 2023Article
- Bridging the gaps in statistical models of protein alignment.Bioinformatics (Oxford, England) · 2022Article
- Application of Homology Modeling by Enhanced Profile-Profile Alignment and Flexible-Fitting Simulation to Cryo-EM Based Structure Determination.International journal of molecular sciences · 2022Article
- New amino acid substitution matrix brings sequence alignments into agreement with structure matches.Proteins · 2021Article
- Rab7D small GTPase is involved in phago-, trogocytosis and cytoskeletal reorganization in the enteric protozoan Entamoeba histolytica.Cellular microbiology · 2021Article
- The ranging of amino acids substitution matrices of various types in accordance with the alignment accuracy criterion.BMC bioinformatics · 2020Article
- Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0.Nature communications · 2020Article
- Crim1Mammalian genome : official journal of the International Mammalian Genome Society · 2019Article
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- Actin Cytoskeletal Reorganization Function of JRAB/MICAL-L2 Is Fine-tuned by Intramolecular Interaction between First LIM Zinc Finger and C-terminal Coiled-coil Domains.Scientific reports · 2019Article
- De novo profile generation based on sequence context specificity with the long short-term memory network.BMC bioinformatics · 2018Article
- Derivative-free neural network for optimizing the scoring functions associated with dynamic programming of pairwise-profile alignment.Algorithms for molecular biology : AMB · 2018Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
motivationAlthough many amino acid substitution matrices have been developed, it has not been well understood which is the best for similarity searches, especially for remote homology detection. Therefore, we collected information related to existing matrices, condensed it and derived a novel matrix that can detect more remote homology than ever.
resultsUsing principal component analysis with existing matrices and benchmarks, we developed a novel matrix, which we designate as MIQS. The detection performance of MIQS is validated and compared with that of existing general purpose matrices using SSEARCH with optimized gap penalties for each matrix. Results show that MIQS is able to detect more remote homology than the existing matrices on an independent dataset. In addition, the performance of our developed matrix was superior to that of CS-BLAST, which was a novel similarity search method with no amino acid matrix. We also evaluated the alignment quality of matrices and methods, which revealed that MIQS shows higher alignment sensitivity than that with the existing matrix series and CS-BLAST. Fundamentally, these results are expected to constitute good proof of the availability and/or importance of amino acid matrices in sequence analysis. Moreover, with our developed matrix, sophisticated similarity search methods such as sequence-profile and profile-profile comparison methods can be improved further. AVAILABILITY AND IMPLEMENTATION: Newly developed matrices and datasets used for this study are available at http://csas.cbrc.jp/Ssearch/.
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