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An optimal mesh algorithm for remote protein homology detection

Remote protein homology detection is a problem of detecting evolutionary relationship between proteins at low sequence similarity level. Among several problems in remote protein homology detection include the questions of determining which combination of multiple alignment and classification techniq...

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Main Authors:	Abdullah, Mohamad Firdaus, Othman, Muhamad Razib, Kasim, Shahreen, Hashim, Rathiah, Hassan, Rohayanti, Asmuni, Hishammuddin, Taliba, Jumail
Format:	Article
Published:	Science and Engineering Research Support Society 2011
Subjects:	QA Mathematics
Online Access:	http://eprints.utm.my/id/eprint/44731/
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spelling	my.utm.447312017-08-30T05:05:11Z http://eprints.utm.my/id/eprint/44731/ An optimal mesh algorithm for remote protein homology detection Abdullah, Mohamad Firdaus Othman, Muhamad Razib Kasim, Shahreen Hashim, Rathiah Hassan, Rohayanti Asmuni, Hishammuddin Taliba, Jumail QA Mathematics Remote protein homology detection is a problem of detecting evolutionary relationship between proteins at low sequence similarity level. Among several problems in remote protein homology detection include the questions of determining which combination of multiple alignment and classification techniques is the best as well as the misalignment of protein sequences during the alignment process. Therefore, this paper deals with remote protein homology detection via assessing the impact of using structural information on protein multiple alignments over sequence information. This paper further presents the best combinations of multiple alignment and classification programs to be chosen. This paper also improves the quality of the multiple alignments via integration of a refinement algorithm. The framework of this paperbegan with datasets preparation on datasets from SCOP version 1.73, followed by multiple alignments of the protein sequences using CLUSTALW, MAFFT, ProbCons and T-Coffee for sequence-based multiple alignments and 3DCoffee, MAMMOTH-mult, MUSTANG and PROMALS3D for structural-based multiple alignments. Next, a refinement algorithm was applied on the protein sequences to reduce misalignments. Lastly, the aligned protein sequences were classified using the pHMMs generative classifier such as HMMER and SAM and also SVMs discriminative classifier such as SVM-Fold and SVM-Struct. The performances of assessed programs were evaluated using ROC, Precision and Recall tests. The result from this paper shows that the combination of refined SVM-Struct and PROMALS3D performs the best against other programs, which suggests that this combination is the best for RPHD. This paper also shows that the use of the refinement algorithm increases the performance of the multiple alignments programs by at least 4%. Science and Engineering Research Support Society 2011 Article PeerReviewed Abdullah, Mohamad Firdaus and Othman, Muhamad Razib and Kasim, Shahreen and Hashim, Rathiah and Hassan, Rohayanti and Asmuni, Hishammuddin and Taliba, Jumail (2011) An optimal mesh algorithm for remote protein homology detection. International Journal of Bio-Science and Bio-Technology, 3 (2). pp. 13-38. ISSN 2233-7849
institution	Universiti Teknologi Malaysia
building	UTM Library
collection	Institutional Repository
continent	Asia
country	Malaysia
content_provider	Universiti Teknologi Malaysia
content_source	UTM Institutional Repository
url_provider	http://eprints.utm.my/
topic	QA Mathematics
spellingShingle	QA Mathematics Abdullah, Mohamad Firdaus Othman, Muhamad Razib Kasim, Shahreen Hashim, Rathiah Hassan, Rohayanti Asmuni, Hishammuddin Taliba, Jumail An optimal mesh algorithm for remote protein homology detection
description	Remote protein homology detection is a problem of detecting evolutionary relationship between proteins at low sequence similarity level. Among several problems in remote protein homology detection include the questions of determining which combination of multiple alignment and classification techniques is the best as well as the misalignment of protein sequences during the alignment process. Therefore, this paper deals with remote protein homology detection via assessing the impact of using structural information on protein multiple alignments over sequence information. This paper further presents the best combinations of multiple alignment and classification programs to be chosen. This paper also improves the quality of the multiple alignments via integration of a refinement algorithm. The framework of this paperbegan with datasets preparation on datasets from SCOP version 1.73, followed by multiple alignments of the protein sequences using CLUSTALW, MAFFT, ProbCons and T-Coffee for sequence-based multiple alignments and 3DCoffee, MAMMOTH-mult, MUSTANG and PROMALS3D for structural-based multiple alignments. Next, a refinement algorithm was applied on the protein sequences to reduce misalignments. Lastly, the aligned protein sequences were classified using the pHMMs generative classifier such as HMMER and SAM and also SVMs discriminative classifier such as SVM-Fold and SVM-Struct. The performances of assessed programs were evaluated using ROC, Precision and Recall tests. The result from this paper shows that the combination of refined SVM-Struct and PROMALS3D performs the best against other programs, which suggests that this combination is the best for RPHD. This paper also shows that the use of the refinement algorithm increases the performance of the multiple alignments programs by at least 4%.
format	Article
author	Abdullah, Mohamad Firdaus Othman, Muhamad Razib Kasim, Shahreen Hashim, Rathiah Hassan, Rohayanti Asmuni, Hishammuddin Taliba, Jumail
author_facet	Abdullah, Mohamad Firdaus Othman, Muhamad Razib Kasim, Shahreen Hashim, Rathiah Hassan, Rohayanti Asmuni, Hishammuddin Taliba, Jumail
author_sort	Abdullah, Mohamad Firdaus
title	An optimal mesh algorithm for remote protein homology detection
title_short	An optimal mesh algorithm for remote protein homology detection
title_full	An optimal mesh algorithm for remote protein homology detection
title_fullStr	An optimal mesh algorithm for remote protein homology detection
title_full_unstemmed	An optimal mesh algorithm for remote protein homology detection
title_sort	optimal mesh algorithm for remote protein homology detection
publisher	Science and Engineering Research Support Society
publishDate	2011
url	http://eprints.utm.my/id/eprint/44731/
_version_	1643651528280506368
score	13.211869

An optimal mesh algorithm for remote protein homology detection

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