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Updated: Dec 9, 2025
A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
SMI-BLAST: a novel supervised search framework based on PSI-BLAST for protein remote homology detection
Xiaopeng Jin1, Qing Liao1, Hang Wei1
1School of Computer Science and Technology, Harbin Institute of Technology, Shenzhen, Guangdong 518055, China.
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.
