Functional equivalency inferred from "authoritative sources" in networks of homologous proteins.
A one-on-one mapping of protein functionality across different species is a critical component of comparative analysis. This paper presents a heuristic algorithm for discovering the Most Likely Functional Counterparts (MoLFunCs) of a protein, based on simple concepts from network theory. A key featu...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2009-06-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC2690840?pdf=render |
| _version_ | 1811211861824110592 |
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| author | Shreedhar Natarajan Eric Jakobsson |
| author_facet | Shreedhar Natarajan Eric Jakobsson |
| author_sort | Shreedhar Natarajan |
| collection | DOAJ |
| description | A one-on-one mapping of protein functionality across different species is a critical component of comparative analysis. This paper presents a heuristic algorithm for discovering the Most Likely Functional Counterparts (MoLFunCs) of a protein, based on simple concepts from network theory. A key feature of our algorithm is utilization of the user's knowledge to assign high confidence to selected functional identification. We show use of the algorithm to retrieve functional equivalents for 7 membrane proteins, from an exploration of almost 40 genomes form multiple online resources. We verify the functional equivalency of our dataset through a series of tests that include sequence, structure and function comparisons. Comparison is made to the OMA methodology, which also identifies one-on-one mapping between proteins from different species. Based on that comparison, we believe that incorporation of user's knowledge as a key aspect of the technique adds value to purely statistical formal methods. |
| first_indexed | 2024-04-12T05:20:29Z |
| format | Article |
| id | doaj.art-bf841671b55c4d7580af30c6286d623c |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-12T05:20:29Z |
| publishDate | 2009-06-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-bf841671b55c4d7580af30c6286d623c2022-12-22T03:46:29ZengPublic Library of Science (PLoS)PLoS ONE1932-62032009-06-0146e589810.1371/journal.pone.0005898Functional equivalency inferred from "authoritative sources" in networks of homologous proteins.Shreedhar NatarajanEric JakobssonA one-on-one mapping of protein functionality across different species is a critical component of comparative analysis. This paper presents a heuristic algorithm for discovering the Most Likely Functional Counterparts (MoLFunCs) of a protein, based on simple concepts from network theory. A key feature of our algorithm is utilization of the user's knowledge to assign high confidence to selected functional identification. We show use of the algorithm to retrieve functional equivalents for 7 membrane proteins, from an exploration of almost 40 genomes form multiple online resources. We verify the functional equivalency of our dataset through a series of tests that include sequence, structure and function comparisons. Comparison is made to the OMA methodology, which also identifies one-on-one mapping between proteins from different species. Based on that comparison, we believe that incorporation of user's knowledge as a key aspect of the technique adds value to purely statistical formal methods.http://europepmc.org/articles/PMC2690840?pdf=render |
| spellingShingle | Shreedhar Natarajan Eric Jakobsson Functional equivalency inferred from "authoritative sources" in networks of homologous proteins. PLoS ONE |
| title | Functional equivalency inferred from "authoritative sources" in networks of homologous proteins. |
| title_full | Functional equivalency inferred from "authoritative sources" in networks of homologous proteins. |
| title_fullStr | Functional equivalency inferred from "authoritative sources" in networks of homologous proteins. |
| title_full_unstemmed | Functional equivalency inferred from "authoritative sources" in networks of homologous proteins. |
| title_short | Functional equivalency inferred from "authoritative sources" in networks of homologous proteins. |
| title_sort | functional equivalency inferred from authoritative sources in networks of homologous proteins |
| url | http://europepmc.org/articles/PMC2690840?pdf=render |
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