Detecting putative orthologs
By Dennis P. Wall, Hunter B. Fraser, Aaron E. Hirsh. 2003
309 citations recorded by the source corpus.
Subfields: Molecular Biology
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In Molecular Biology
- Steven Kelly
- David M. Emms
- Christophe Dessimoz
- Adrian M. Altenhoff
- Aaron J. Mackey
- Feng Chen
- Jeroen K. Vermunt
- David S. Roos
Citations in the corpus
- Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes (2007, methodology): “; methods based on evolutionary distance metrics include RSD (Reciprocal Smallest Distance)”
- OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy (2015, methodology): “best BLAST hit (RBH) as it is widely regarded as a high precision method for the identification of orthologues gene-pairs [25–27].”
- Protein complex prediction with AlphaFold-Multimer (2021, background): “Cross-Chain Genetics Identifying pairwise correlation in an MSA requires prior determination and alignment of interacting homologs in the heteromeric case, which is in general ambiguous [11].”
- Choosing BLAST options for better detection of orthologs as reciprocal best hits (2008, methodology): “…DISTANCES BARELY DETECT MORE ORTHOLOGS THAN RECIPROCAL BEST HITS Since we wanted to have a control, a ceiling, of the expected number of orthologs, we tested the RSD definition of orthology , because it was reported to produce a much higher number of orthologs than RBHs (Wall et al., 2003).”
- Computed structures of core eukaryotic protein complexes (2021, unknown): “We compared the sequences for each protein in each of the additional 4325 proteomes against those of the most closely related species in the OrthoDB database and used the reciprocal best hit criterion ( 20 ) to identify orthologs (fig.”
- Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods (2009, result): “Finally, we also compare the results to the standard approaches of bidirectional best-hits (BBH) [21], common in ad-hoc analyses, and reciprocal smallest distance (RSD) [ 22 ].”