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SAROTUP: a suite of tools for finding potential target-unrelated peptides from phage display data

SAROTUP (Scanner And Reporter Of Target-Unrelated Peptides) 3.1 is a significant upgrade to the widely used SAROTUP web server for the rapid identification of target-unrelated peptides (TUPs) in phage display data. At present, SAROTUP has gathered a suite of tools for finding potential TUPs and othe...

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Detalles Bibliográficos
Autores principales: He, Bifang, Chen, Heng, Li, Ning, Huang, Jian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Ivyspring International Publisher 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6643146/
https://www.ncbi.nlm.nih.gov/pubmed/31337975
http://dx.doi.org/10.7150/ijbs.31957
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author He, Bifang
Chen, Heng
Li, Ning
Huang, Jian
author_facet He, Bifang
Chen, Heng
Li, Ning
Huang, Jian
author_sort He, Bifang
collection PubMed
description SAROTUP (Scanner And Reporter Of Target-Unrelated Peptides) 3.1 is a significant upgrade to the widely used SAROTUP web server for the rapid identification of target-unrelated peptides (TUPs) in phage display data. At present, SAROTUP has gathered a suite of tools for finding potential TUPs and other purposes. Besides the TUPScan, the motif-based tool, and three tools based on the BDB database, i.e., MimoScan, MimoSearch, and MimoBlast, three predictors based on support vector machine, i.e., PhD7Faster, SABinder and PSBinder, are integrated into SAROTUP. The current version of SAROTUP contains 27 TUP motifs and 823 TUP sequences. We also developed the standalone SAROTUP application with graphical user interface (GUI) and command line versions for processing deep sequencing phage display data and distributed it as an open source package, which can perform perfectly locally on almost all systems that support C++ with little or no modification. The web interfaces of SAROTUP have also been redesigned to be more self-evident and user-friendly. The latest version of SAROTUP is freely available at http://i.uestc.edu.cn/sarotup3.
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spelling pubmed-66431462019-07-23 SAROTUP: a suite of tools for finding potential target-unrelated peptides from phage display data He, Bifang Chen, Heng Li, Ning Huang, Jian Int J Biol Sci Research Paper SAROTUP (Scanner And Reporter Of Target-Unrelated Peptides) 3.1 is a significant upgrade to the widely used SAROTUP web server for the rapid identification of target-unrelated peptides (TUPs) in phage display data. At present, SAROTUP has gathered a suite of tools for finding potential TUPs and other purposes. Besides the TUPScan, the motif-based tool, and three tools based on the BDB database, i.e., MimoScan, MimoSearch, and MimoBlast, three predictors based on support vector machine, i.e., PhD7Faster, SABinder and PSBinder, are integrated into SAROTUP. The current version of SAROTUP contains 27 TUP motifs and 823 TUP sequences. We also developed the standalone SAROTUP application with graphical user interface (GUI) and command line versions for processing deep sequencing phage display data and distributed it as an open source package, which can perform perfectly locally on almost all systems that support C++ with little or no modification. The web interfaces of SAROTUP have also been redesigned to be more self-evident and user-friendly. The latest version of SAROTUP is freely available at http://i.uestc.edu.cn/sarotup3. Ivyspring International Publisher 2019-06-02 /pmc/articles/PMC6643146/ /pubmed/31337975 http://dx.doi.org/10.7150/ijbs.31957 Text en © Ivyspring International Publisher This is an open access article distributed under the terms of the Creative Commons Attribution (CC BY-NC) license (https://creativecommons.org/licenses/by-nc/4.0/). See http://ivyspring.com/terms for full terms and conditions.
spellingShingle Research Paper
He, Bifang
Chen, Heng
Li, Ning
Huang, Jian
SAROTUP: a suite of tools for finding potential target-unrelated peptides from phage display data
title SAROTUP: a suite of tools for finding potential target-unrelated peptides from phage display data
title_full SAROTUP: a suite of tools for finding potential target-unrelated peptides from phage display data
title_fullStr SAROTUP: a suite of tools for finding potential target-unrelated peptides from phage display data
title_full_unstemmed SAROTUP: a suite of tools for finding potential target-unrelated peptides from phage display data
title_short SAROTUP: a suite of tools for finding potential target-unrelated peptides from phage display data
title_sort sarotup: a suite of tools for finding potential target-unrelated peptides from phage display data
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6643146/
https://www.ncbi.nlm.nih.gov/pubmed/31337975
http://dx.doi.org/10.7150/ijbs.31957
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