New alignment method for remote protein sequences by the direct use of pairwise sequence correlations and substitutions
Understanding protein sequences and how they relate to the functions of proteins is extremely important. One of the most basic operations in bioinformatics is sequence alignment and usually the first things learned from these are which positions are the most conserved and often these are critical pa...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-10-01
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| Series: | Frontiers in Bioinformatics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fbinf.2023.1227193/full |
| _version_ | 1797660919637999616 |
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| author | Kejue Jia Mesih Kilinc Mesih Kilinc Robert L. Jernigan Robert L. Jernigan |
| author_facet | Kejue Jia Mesih Kilinc Mesih Kilinc Robert L. Jernigan Robert L. Jernigan |
| author_sort | Kejue Jia |
| collection | DOAJ |
| description | Understanding protein sequences and how they relate to the functions of proteins is extremely important. One of the most basic operations in bioinformatics is sequence alignment and usually the first things learned from these are which positions are the most conserved and often these are critical parts of the structure, such as enzyme active site residues. In addition, the contact pairs in a protein usually correspond closely to the correlations between residue positions in the multiple sequence alignment, and these usually change in a systematic and coordinated way, if one position changes then the other member of the pair also changes to compensate. In the present work, these correlated pairs are taken as anchor points for a new type of sequence alignment. The main advantage of the method here is its combining the remote homolog detection from our method PROST with pairwise sequence substitutions in the rigorous method from Kleinjung et al. We show a few examples of some resulting sequence alignments, and how they can lead to improvements in alignments for function, even for a disordered protein. |
| first_indexed | 2024-03-11T18:36:53Z |
| format | Article |
| id | doaj.art-61a72fcba7724addb1f980b2c75d0dd6 |
| institution | Directory Open Access Journal |
| issn | 2673-7647 |
| language | English |
| last_indexed | 2024-03-11T18:36:53Z |
| publishDate | 2023-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Bioinformatics |
| spelling | doaj.art-61a72fcba7724addb1f980b2c75d0dd62023-10-12T17:02:38ZengFrontiers Media S.A.Frontiers in Bioinformatics2673-76472023-10-01310.3389/fbinf.2023.12271931227193New alignment method for remote protein sequences by the direct use of pairwise sequence correlations and substitutionsKejue Jia0Mesih Kilinc1Mesih Kilinc2Robert L. Jernigan3Robert L. Jernigan4Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United StatesRoy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United StatesBioinformatics and Computational Biology Program, Iowa State University, Ames, IA, United StatesRoy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United StatesBioinformatics and Computational Biology Program, Iowa State University, Ames, IA, United StatesUnderstanding protein sequences and how they relate to the functions of proteins is extremely important. One of the most basic operations in bioinformatics is sequence alignment and usually the first things learned from these are which positions are the most conserved and often these are critical parts of the structure, such as enzyme active site residues. In addition, the contact pairs in a protein usually correspond closely to the correlations between residue positions in the multiple sequence alignment, and these usually change in a systematic and coordinated way, if one position changes then the other member of the pair also changes to compensate. In the present work, these correlated pairs are taken as anchor points for a new type of sequence alignment. The main advantage of the method here is its combining the remote homolog detection from our method PROST with pairwise sequence substitutions in the rigorous method from Kleinjung et al. We show a few examples of some resulting sequence alignments, and how they can lead to improvements in alignments for function, even for a disordered protein.https://www.frontiersin.org/articles/10.3389/fbinf.2023.1227193/fullprotein sequencessequence alignment algorithmcoevolution informationdisordered proteinsfunction from sequence alignment |
| spellingShingle | Kejue Jia Mesih Kilinc Mesih Kilinc Robert L. Jernigan Robert L. Jernigan New alignment method for remote protein sequences by the direct use of pairwise sequence correlations and substitutions Frontiers in Bioinformatics protein sequences sequence alignment algorithm coevolution information disordered proteins function from sequence alignment |
| title | New alignment method for remote protein sequences by the direct use of pairwise sequence correlations and substitutions |
| title_full | New alignment method for remote protein sequences by the direct use of pairwise sequence correlations and substitutions |
| title_fullStr | New alignment method for remote protein sequences by the direct use of pairwise sequence correlations and substitutions |
| title_full_unstemmed | New alignment method for remote protein sequences by the direct use of pairwise sequence correlations and substitutions |
| title_short | New alignment method for remote protein sequences by the direct use of pairwise sequence correlations and substitutions |
| title_sort | new alignment method for remote protein sequences by the direct use of pairwise sequence correlations and substitutions |
| topic | protein sequences sequence alignment algorithm coevolution information disordered proteins function from sequence alignment |
| url | https://www.frontiersin.org/articles/10.3389/fbinf.2023.1227193/full |
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