SMI-BLAST: a novel supervised search framework based on PSI-BLAST for protein remote homology detection.

Xiaopeng Jin, Qing Liao, Hang Wei, Jun Zhang, Bin Liu

Bioinformatics (Oxford, England) 2021 May 17

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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. 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. 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 data are available at Bioinformatics online. © The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Citation

Xiaopeng Jin, Qing Liao, Hang Wei, Jun Zhang, Bin Liu. SMI-BLAST: a novel supervised search framework based on PSI-BLAST for protein remote homology detection. Bioinformatics (Oxford, England). 2021 May 17;37(7):913-920