TY - JOUR

T1 - Duo

T2 - A Signature Based Method to Batch-Analyze Functional Similarities of Proteins

AU - Fei, Xiao

AU - Li, Qiuchun

AU - Olsen, John Elmerdahl

AU - Jiao, Xinan

N1 - Publisher Copyright: © Copyright © 2021 Fei, Li, Olsen and Jiao.

PY - 2021

Y1 - 2021

N2 - With the rapid advancement of sequencing technology, handling of large sequencing data to analyze for protein coding capacity and functionality of predicted proteins has become an urgent demand. There is a lack of simple and effective tools to functionally annotate large number of unknown proteins in a personalized and customized workflow. To address this, we developed Duo, which batch-analyze functional similarities of predicted proteins. Duo can screen query proteins with specific characteristics based on highly flexible and customizable reference inputs from the user. In the current study, Duo was applied to screen for virulence associated proteins in the genome-sequence of Salmonella Typhimurium. Based on the analysis, recommendation for choice of Seed_database in order to get a reasonable number of predicted proteins for further analysis, and recommendation for preparing a Reference_proteins set for Duo was given. Delta-bitscore analysis was shown to be useful tool to focus the follow-up on predicted proteins. A successful screen for virulence proteins in the bacterial genome-sequence was further performed in a selection of 32 pathogenic bacteria, documenting the ability of Duo to work on a broad collection of bacteria. We anticipate that Duo will be a useful auxiliary tool for personalized and customized protein function research in the future.

AB - With the rapid advancement of sequencing technology, handling of large sequencing data to analyze for protein coding capacity and functionality of predicted proteins has become an urgent demand. There is a lack of simple and effective tools to functionally annotate large number of unknown proteins in a personalized and customized workflow. To address this, we developed Duo, which batch-analyze functional similarities of predicted proteins. Duo can screen query proteins with specific characteristics based on highly flexible and customizable reference inputs from the user. In the current study, Duo was applied to screen for virulence associated proteins in the genome-sequence of Salmonella Typhimurium. Based on the analysis, recommendation for choice of Seed_database in order to get a reasonable number of predicted proteins for further analysis, and recommendation for preparing a Reference_proteins set for Duo was given. Delta-bitscore analysis was shown to be useful tool to focus the follow-up on predicted proteins. A successful screen for virulence proteins in the bacterial genome-sequence was further performed in a selection of 32 pathogenic bacteria, documenting the ability of Duo to work on a broad collection of bacteria. We anticipate that Duo will be a useful auxiliary tool for personalized and customized protein function research in the future.

KW - bacteria

KW - biological signature

KW - hidden Markov models

KW - protein

KW - Salmonella

U2 - 10.3389/fmicb.2021.698322

DO - 10.3389/fmicb.2021.698322

M3 - Journal article

C2 - 34475860

AN - SCOPUS:85114213646

VL - 12

JO - Frontiers in Microbiology

JF - Frontiers in Microbiology

SN - 1664-302X

M1 - 698322

ER -