|Table of Contents|

Benchmarking Fast Homology Search Softwares Based on Model Organisms(PDF)

《南京师大学报（自然科学版）》[ISSN:1001-4616/CN:32-1239/N]

Issue:
2022年02期
Page:
44-51
Research Field:
·生物学·
Publishing date:

Info

Title:
Benchmarking Fast Homology Search Softwares Based on Model Organisms
Author(s):
Wang Yinwei; Wu Jingjing; Zhang Chenning; Hua Yijia; Li Peng; Yan Jie
(School of Life Sciences,Nanjing Normal University,Nanjing 210023,China)
Keywords:
homology search; orthology inference; RBH; fast algorithms; sequence comparision
PACS:
Q33
DOI:
10.3969/j.issn.1001-4616.2022.02.006
Abstract:
Blastp in the traditional blast+package has been extremely slow in the era of big data. The development of homology search software has made great progress in the past decade or so,but comprehensive uations are scarce. In this study,a comprehensive comparison between 7 fast homology search softwares and blastp was conducted,and it was found that fast mode in diamond is generally faster than the others and has the lowest false discover rate. In memory consumption,MMseqs2 is the lowest while ghostx is the highest. In terms of the number of identified hits,s7.5 mode in MMseqs2 had the highest number at medium Genomic Similarity Scores(GSS)except blastp,but the s5 model should be a better choice. As GSS decreases,ghostx obtains the most results,while ublast obtains the most results as GSS increases. In terms of the number of identified Reciprocal Best Hits(RBH),ghostx has an advantage in remote search,and this advantage is also supported by synteny evidence. In terms of homology search,there is a large overlap among almost all software,with the exception of ghostx,which has 43.4% additional results and the highest false discovery rate while s3 mode in MMseqs2 has the lowest. Overall,compared to blastp,MMseqs2,diamond and ghostx are the three best alternatives to blastp. Diamond is well suited for orthology inference and can search accurately and quickly in “fast” mode,and “very” is the best search mode on balance,but for remote search,ghostx is more advantageous,while for identification of homologous proteins at medium GSS,s5 mode in MMseqs2 may be a good choice.

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