| 1. |
- Forslund, Kristoffer, et al.
(författare)
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OrthoDisease : tracking disease gene orthologs across 100 species
- 2011
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Ingår i: Briefings in Bioinformatics. - : Oxford University Press (OUP). - 1467-5463 .- 1477-4054. ; 12:5, s. 463-473
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Tidskriftsartikel (refereegranskat)abstract
- Orthology is one of the most important tools available to modern biology, as it allows making inferences from easily studied model systems to much less tractable systems of interest, such as ourselves. This becomes important not least in the study of genetic diseases. We here review work on the orthology of disease-associated genes and also present an updated version of the InParanoid-based disease orthology database and web site OrthoDisease, with 14-fold increased species coverage since the previous version. Using this resource, we survey the taxonomic distribution of orthologs of human genes involved in different disease categories. The hypothesis that paralogs can mask the effect of deleterious mutations predicts that known heritable disease genes should have fewer close paralogs. We found large-scale support for this hypothesis as significantly fewer duplications were observed for disease genes in the OrthoDisease ortholog groups.
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| 2. |
- Schmitt, Thomas, et al.
(författare)
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Letter to the Editor : SeqXML and OrthoXML: standards for sequence and orthology information
- 2011
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Ingår i: Briefings in Bioinformatics. - : Oxford University Press (OUP). - 1467-5463 .- 1477-4054. ; 12:5, s. 485-488
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Tidskriftsartikel (refereegranskat)abstract
- There is a great need for standards in the orthology field. Users must contend with different ortholog data representations from each provider, and the providers themselves must independently gather and parse the input sequence data. These burdensome and redundant procedures make data comparison and integration difficult. We have designed two XML-based formats, SeqXML and OrthoXML, to solve these problems. SeqXML is a lightweight format for sequence records the input for orthology prediction. It stores the same sequence and metadata as typical FASTA format records, but overcomes common problems such as unstructured metadata in the header and erroneous sequence content. XML provides validation to prevent data integrity problems that are frequent in FASTA files. The range of applications for SeqXML is broad and not limited to ortholog prediction. We provide read/write functions for BioJava, BioPerl, and Biopython. OrthoXML was designed to represent ortholog assignments from any source in a consistent and structured way, yet cater to specific needs such as scoring schemes or meta-information. A unified format is particularly valuable for ortholog consumers that want to integrate data from numerous resources, e. g. for gene annotation projects. Reference proteomes for 61 organisms are already available in SeqXML, and 10 orthology databases have signed on to OrthoXML. Adoption by the entire field would substantially facilitate exchange and quality control of sequence and orthology information.
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| 3. |
- Schreiber, Fabian, et al.
(författare)
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Hieranoid : Hierarchical Orthology Inference
- 2013
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Ingår i: Journal of Molecular Biology. - : Elsevier BV. - 0022-2836 .- 1089-8638. ; 425:11, s. 2072-2081
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Tidskriftsartikel (refereegranskat)abstract
- An accurate inference of orthologs is essential in many research fields such as comparative genomics, molecular evolution, and genome annotation. Existing methods for genome-scale orthology inference are mostly based on all-versus-all similarity searches that scale quadratically with the number of species. This limits their application to the increasing number of available large-scale datasets. Here, we present Hieranoid, a new orthology inference method using a hierarchical approach. Hieranoid performs pairwise orthology analysis using In Paranoid at each node in a guide tree as it progresses from its leaves to the root. This concept reduces the total runtime complexity from a quadratic to a linear function of the number of species. The tree hierarchy provides a natural structure in multi-species ortholog groups, and the aggregation of multiple sequences allows for multiple alignment similarity searching techniques, which can yield more accurate ortholog groups. Using the recently published orthobench benchmark, Hieranoid showed the overall best performance. Our progressive approach presents a new way to infer orthologs that combines efficient graph-based methodology with aspects of compute-intensive tree-based methods. The linear scaling with the number of species is a major advantage for large-scale applications and makes Hieranoid well suited to cope with vast amounts of sequenced genomes in the future. Hieranoid is an open source and can be downloaded at Hieranoid.sbc.su.se. (C) 2013 Elsevier Ltd. All rights reserved.
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