OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation
Orthology relations can be used to transfer annotations from one gene (or protein) to another. Hence, detecting orthology relations has become an important task in the post-genomic era. Various genomic events, such as duplication and horizontal gene transfer, can cause erroneous assignment of orthol...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2017-12-01
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| Series: | Genomics, Proteomics & Bioinformatics |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1672022917301663 |
| _version_ | 1797368033892630528 |
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| author | Soheil Jahangiri-Tazehkand Limsoon Wong Changiz Eslahchi |
| author_facet | Soheil Jahangiri-Tazehkand Limsoon Wong Changiz Eslahchi |
| author_sort | Soheil Jahangiri-Tazehkand |
| collection | DOAJ |
| description | Orthology relations can be used to transfer annotations from one gene (or protein) to another. Hence, detecting orthology relations has become an important task in the post-genomic era. Various genomic events, such as duplication and horizontal gene transfer, can cause erroneous assignment of orthology relations. In closely-related species, gene neighborhood information can be used to resolve many ambiguities in orthology inference. Here we present OrthoGNC, a software for accurately predicting pairwise orthology relations based on gene neighborhood conservation. Analyses on simulated and real data reveal the high accuracy of OrthoGNC. In addition to orthology detection, OrthoGNC can be employed to investigate the conservation of genomic context among potential orthologs detected by other methods. OrthoGNC is freely available online at http://bs.ipm.ir/softwares/orthognc and http://tinyurl.com/orthoGNC. |
| first_indexed | 2024-03-08T17:26:42Z |
| format | Article |
| id | doaj.art-80fd39c7073e48ca8b5253c6251701e4 |
| institution | Directory Open Access Journal |
| issn | 1672-0229 |
| language | English |
| last_indexed | 2024-03-08T17:26:42Z |
| publishDate | 2017-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Genomics, Proteomics & Bioinformatics |
| spelling | doaj.art-80fd39c7073e48ca8b5253c6251701e42024-01-02T18:46:11ZengElsevierGenomics, Proteomics & Bioinformatics1672-02292017-12-0115636137010.1016/j.gpb.2017.07.002OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood ConservationSoheil Jahangiri-Tazehkand0Limsoon Wong1Changiz Eslahchi2Department of Computer Science, Shahid Beheshti University, Tehran 1983969411, IranSchool of Computing, National University of Singapore, Singapore 117417, SingaporeDepartment of Computer Science, Shahid Beheshti University, Tehran 1983969411, IranOrthology relations can be used to transfer annotations from one gene (or protein) to another. Hence, detecting orthology relations has become an important task in the post-genomic era. Various genomic events, such as duplication and horizontal gene transfer, can cause erroneous assignment of orthology relations. In closely-related species, gene neighborhood information can be used to resolve many ambiguities in orthology inference. Here we present OrthoGNC, a software for accurately predicting pairwise orthology relations based on gene neighborhood conservation. Analyses on simulated and real data reveal the high accuracy of OrthoGNC. In addition to orthology detection, OrthoGNC can be employed to investigate the conservation of genomic context among potential orthologs detected by other methods. OrthoGNC is freely available online at http://bs.ipm.ir/softwares/orthognc and http://tinyurl.com/orthoGNC.http://www.sciencedirect.com/science/article/pii/S1672022917301663OrthologyHomologyGene neighborhood conservationGenomic contextComparative genomics |
| spellingShingle | Soheil Jahangiri-Tazehkand Limsoon Wong Changiz Eslahchi OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation Genomics, Proteomics & Bioinformatics Orthology Homology Gene neighborhood conservation Genomic context Comparative genomics |
| title | OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation |
| title_full | OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation |
| title_fullStr | OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation |
| title_full_unstemmed | OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation |
| title_short | OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation |
| title_sort | orthognc a software for accurate identification of orthologs based on gene neighborhood conservation |
| topic | Orthology Homology Gene neighborhood conservation Genomic context Comparative genomics |
| url | http://www.sciencedirect.com/science/article/pii/S1672022917301663 |
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