PhD7Faster 2.0: predicting clones propagating faster from the Ph.D.-7 phage display library by coupling PseAAC and tripeptide composition
Selection from phage display libraries empowers isolation of high-affinity ligands for various targets. However, this method also identifies propagation-related target-unrelated peptides (PrTUPs). These false positive hits appear because of their amplification advantages. In this report, we present...
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2019-06-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/7131.pdf |
| _version_ | 1797424237916454912 |
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| author | Bifang He Heng Chen Jian Huang |
| author_facet | Bifang He Heng Chen Jian Huang |
| author_sort | Bifang He |
| collection | DOAJ |
| description | Selection from phage display libraries empowers isolation of high-affinity ligands for various targets. However, this method also identifies propagation-related target-unrelated peptides (PrTUPs). These false positive hits appear because of their amplification advantages. In this report, we present PhD7Faster 2.0 for predicting fast-propagating clones from the Ph.D.-7 phage display library, which was developed based on the support vector machine. Feature selection was performed against PseAAC and tripeptide composition using the incremental feature selection method. Ten-fold cross-validation results show that PhD7Faster 2.0 succeeds a decent performance with the accuracy of 81.84%, the Matthews correlation coefficient of 0.64 and the area under the ROC curve of 0.90. The permutation test with 1,000 shuffles resulted in p < 0.001. We implemented PhD7Faster 2.0 into a publicly accessible web tool (http://i.uestc.edu.cn/sarotup3/cgi-bin/PhD7Faster.pl) and constructed standalone graphical user interface and command-line versions for different systems. The standalone PhD7Faster 2.0 is able to detect PrTUPs within small datasets as well as large-scale datasets. This makes PhD7Faster 2.0 an enhanced and powerful tool for scanning and reporting faster-growing clones from the Ph.D.-7 phage display library. |
| first_indexed | 2024-03-09T07:58:20Z |
| format | Article |
| id | doaj.art-366c92a40d3b4c11a4147fc4685c733d |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T07:58:20Z |
| publishDate | 2019-06-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
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| spelling | doaj.art-366c92a40d3b4c11a4147fc4685c733d2023-12-03T00:49:28ZengPeerJ Inc.PeerJ2167-83592019-06-017e713110.7717/peerj.7131PhD7Faster 2.0: predicting clones propagating faster from the Ph.D.-7 phage display library by coupling PseAAC and tripeptide compositionBifang He0Heng Chen1Jian Huang2School of Medicine, Guizhou University, Guiyang, Guizhou, ChinaSchool of Medicine, Guizhou University, Guiyang, Guizhou, ChinaCenter for Informational Biology, University of Electronic Science and Technology of China, Chengdu, Sichuan, ChinaSelection from phage display libraries empowers isolation of high-affinity ligands for various targets. However, this method also identifies propagation-related target-unrelated peptides (PrTUPs). These false positive hits appear because of their amplification advantages. In this report, we present PhD7Faster 2.0 for predicting fast-propagating clones from the Ph.D.-7 phage display library, which was developed based on the support vector machine. Feature selection was performed against PseAAC and tripeptide composition using the incremental feature selection method. Ten-fold cross-validation results show that PhD7Faster 2.0 succeeds a decent performance with the accuracy of 81.84%, the Matthews correlation coefficient of 0.64 and the area under the ROC curve of 0.90. The permutation test with 1,000 shuffles resulted in p < 0.001. We implemented PhD7Faster 2.0 into a publicly accessible web tool (http://i.uestc.edu.cn/sarotup3/cgi-bin/PhD7Faster.pl) and constructed standalone graphical user interface and command-line versions for different systems. The standalone PhD7Faster 2.0 is able to detect PrTUPs within small datasets as well as large-scale datasets. This makes PhD7Faster 2.0 an enhanced and powerful tool for scanning and reporting faster-growing clones from the Ph.D.-7 phage display library.https://peerj.com/articles/7131.pdfPropagation-related TUPsPh.D.-7 phage display libraryPredictorFeature selectionSupport vector machine |
| spellingShingle | Bifang He Heng Chen Jian Huang PhD7Faster 2.0: predicting clones propagating faster from the Ph.D.-7 phage display library by coupling PseAAC and tripeptide composition PeerJ Propagation-related TUPs Ph.D.-7 phage display library Predictor Feature selection Support vector machine |
| title | PhD7Faster 2.0: predicting clones propagating faster from the Ph.D.-7 phage display library by coupling PseAAC and tripeptide composition |
| title_full | PhD7Faster 2.0: predicting clones propagating faster from the Ph.D.-7 phage display library by coupling PseAAC and tripeptide composition |
| title_fullStr | PhD7Faster 2.0: predicting clones propagating faster from the Ph.D.-7 phage display library by coupling PseAAC and tripeptide composition |
| title_full_unstemmed | PhD7Faster 2.0: predicting clones propagating faster from the Ph.D.-7 phage display library by coupling PseAAC and tripeptide composition |
| title_short | PhD7Faster 2.0: predicting clones propagating faster from the Ph.D.-7 phage display library by coupling PseAAC and tripeptide composition |
| title_sort | phd7faster 2 0 predicting clones propagating faster from the ph d 7 phage display library by coupling pseaac and tripeptide composition |
| topic | Propagation-related TUPs Ph.D.-7 phage display library Predictor Feature selection Support vector machine |
| url | https://peerj.com/articles/7131.pdf |
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