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dc.contributor.authorMahmood, K
dc.contributor.authorWebb, GI
dc.contributor.authorSong, J
dc.contributor.authorWhisstock, JC
dc.contributor.authorKonagurthu, AS
dc.date.accessioned2020-12-10T00:49:08Z
dc.date.available2020-12-10T00:49:08Z
dc.date.issued2012-03-01
dc.identifierpii: gkr1261
dc.identifier.citationMahmood, K., Webb, G. I., Song, J., Whisstock, J. C. & Konagurthu, A. S. (2012). Efficient large-scale protein sequence comparison and gene matching to identify orthologs and co-orthologs. NUCLEIC ACIDS RESEARCH, 40 (6), https://doi.org/10.1093/nar/gkr1261.
dc.identifier.issn0305-1048
dc.identifier.urihttp://hdl.handle.net/11343/253582
dc.description.abstractBroadly, computational approaches for ortholog assignment is a three steps process: (i) identify all putative homologs between the genomes, (ii) identify gene anchors and (iii) link anchors to identify best gene matches given their order and context. In this article, we engineer two methods to improve two important aspects of this pipeline [specifically steps (ii) and (iii)]. First, computing sequence similarity data [step (i)] is a computationally intensive task for large sequence sets, creating a bottleneck in the ortholog assignment pipeline. We have designed a fast and highly scalable sort-join method (afree) based on k-mer counts to rapidly compare all pairs of sequences in a large protein sequence set to identify putative homologs. Second, availability of complex genomes containing large gene families with prevalence of complex evolutionary events, such as duplications, has made the task of assigning orthologs and co-orthologs difficult. Here, we have developed an iterative graph matching strategy where at each iteration the best gene assignments are identified resulting in a set of orthologs and co-orthologs. We find that the afree algorithm is faster than existing methods and maintains high accuracy in identifying similar genes. The iterative graph matching strategy also showed high accuracy in identifying complex gene relationships. Standalone afree available from http://vbc.med.monash.edu.au/∼kmahmood/afree. EGM2, complete ortholog assignment pipeline (including afree and the iterative graph matching method) available from http://vbc.med.monash.edu.au/∼kmahmood/EGM2.
dc.languageEnglish
dc.publisherOXFORD UNIV PRESS
dc.rights.urihttps://creativecommons.org/licenses/by-nc/4.0
dc.titleEfficient large-scale protein sequence comparison and gene matching to identify orthologs and co-orthologs
dc.typeJournal Article
dc.identifier.doi10.1093/nar/gkr1261
melbourne.affiliation.departmentMedicine Dentistry & Health Sciences
melbourne.source.titleNucleic Acids Research
melbourne.source.volume40
melbourne.source.issue6
dc.rights.licenseCC BY-NC
melbourne.elementsid1322399
melbourne.contributor.authorMahmood, Khalid
dc.identifier.eissn1362-4962
melbourne.accessrightsOpen Access


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