PMID- 32898222
OWN - NLM
STAT- MEDLINE
DCOM- 20210608
LR  - 20210608
IS  - 1367-4811 (Electronic)
IS  - 1367-4803 (Linking)
VI  - 37
IP  - 7
DP  - 2021 May 17
TI  - SMI-BLAST: a novel supervised search framework based on PSI-BLAST for protein 
      remote homology detection.
PG  - 913-920
LID - 10.1093/bioinformatics/btaa772 [doi]
AB  - 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.
CI  - (c) The Author(s) 2020. Published by Oxford University Press. All rights reserved. 
      For permissions, please e-mail: journals.permissions@oup.com.
FAU - Jin, Xiaopeng
AU  - Jin X
AD  - School of Computer Science and Technology, Harbin Institute of Technology, 
      Shenzhen, Guangdong 518055, China.
FAU - Liao, Qing
AU  - Liao Q
AD  - School of Computer Science and Technology, Harbin Institute of Technology, 
      Shenzhen, Guangdong 518055, China.
FAU - Wei, Hang
AU  - Wei H
AD  - School of Computer Science and Technology, Harbin Institute of Technology, 
      Shenzhen, Guangdong 518055, China.
FAU - Zhang, Jun
AU  - Zhang J
AD  - School of Computer Science and Technology, Harbin Institute of Technology, 
      Shenzhen, Guangdong 518055, China.
FAU - Liu, Bin
AU  - Liu B
AD  - School of Computer Science and Technology, Harbin Institute of Technology, 
      Shenzhen, Guangdong 518055, China.
AD  - School of Computer Science and Technology, Beijing Institute of Technology, 
      Beijing 100081, China.
AD  - Advanced Research Institute of Multidisciplinary Science, Beijing Institute of 
      Technology, Beijing 100081, China.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - England
TA  - Bioinformatics
JT  - Bioinformatics (Oxford, England)
JID - 9808944
RN  - 0 (Proteins)
SB  - IM
MH  - *Algorithms
MH  - Amino Acid Sequence
MH  - Position-Specific Scoring Matrices
MH  - *Proteins
MH  - Sequence Alignment
MH  - Sequence Analysis, Protein
EDAT- 2020/09/09 06:00
MHDA- 2021/06/09 06:00
CRDT- 2020/09/08 17:13
PHST- 2020/05/21 00:00 [received]
PHST- 2020/08/14 00:00 [revised]
PHST- 2020/08/28 00:00 [accepted]
PHST- 2020/09/09 06:00 [pubmed]
PHST- 2021/06/09 06:00 [medline]
PHST- 2020/09/08 17:13 [entrez]
AID - 5902827 [pii]
AID - 10.1093/bioinformatics/btaa772 [doi]
PST - ppublish
SO  - Bioinformatics. 2021 May 17;37(7):913-920. doi: 10.1093/bioinformatics/btaa772.