Jin X, Liao Q, Wei H, Zhang J, Liu B. SMI-BLAST: a novel supervised search framework based on PSI-BLAST for protein remote homology detection.
Bioinformatics 2021;
37:913-920. [PMID:
32898222 DOI:
10.1093/bioinformatics/btaa772]
[Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/14/2020] [Accepted: 08/28/2020] [Indexed: 12/11/2022] Open
Abstract
MOTIVATION
As one of the most important and widely used mainstream iterative search tool for protein sequence search, an accurate Position-Specific Scoring Matrix (PSSM) is the key of PSI-BLAST. However, PSSMs containing non-homologous information obviously reduce the performance of PSI-BLAST for protein remote homology.
RESULTS
To further study this problem, we summarize three types of Incorrectly Selected Homology (ISH) errors in PSSMs. A new search tool Supervised-Manner-based Iterative BLAST (SMI-BLAST) is proposed based on PSI-BLAST for solving these errors. SMI-BLAST obviously outperforms PSI-BLAST on the Structural Classification of Proteins-extended (SCOPe) dataset. Compared with PSI-BLAST on the ISH error subsets of SCOPe dataset, SMI-BLAST detects 1.6-2.87 folds more remote homologous sequences, and outperforms PSI-BLAST by 35.66% in terms of ROC1 scores. Furthermore, this framework is applied to JackHMMER, DELTA-BLAST and PSI-BLASTexB, and their performance is further improved.
AVAILABILITY AND IMPLEMENTATION
User-friendly webservers for SMI-BLAST, JackHMMER, DELTA-BLAST and PSI-BLASTexB are established at http://bliulab.net/SMI-BLAST/, by which the users can easily get the results without the need to go through the mathematical details.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
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