doi: 10.1093/bioinformatics/btg213.
Detecting putative orthologs
Affiliations
- PMID: 15593400
- DOI: 10.1093/bioinformatics/btg213
Item in Clipboard
Detecting putative orthologs
Bioinformatics.
.
Abstract
We developed an algorithm that improves upon the common procedure of taking reciprocal best blast hits(rbh) in the identification of orthologs. The method-reciprocal smallest distance algorithm (rsd)-relies on global sequence alignment and maximum likelihood estimation of evolutionary distances to detect orthologs between two genomes. rsd finds many putative orthologs missed by rbh because it is less likely than rbh to be misled by the presence of a close paralog.
Similar articles
-
Ortholog detection using the reciprocal smallest distance algorithm.Methods Mol Biol. 2007;396:95-110. doi: 10.1007/978-1-59745-515-2_7. Methods Mol Biol. 2007. PMID: 18025688
-
Choosing BLAST options for better detection of orthologs as reciprocal best hits.Bioinformatics. 2008 Feb 1;24(3):319-24. doi: 10.1093/bioinformatics/btm585. Epub 2007 Nov 26. Bioinformatics. 2008. PMID: 18042555
-
Progress in quickly finding orthologs as reciprocal best hits: comparing blast, last, diamond and MMseqs2.BMC Genomics. 2020 Oct 24;21(1):741. doi: 10.1186/s12864-020-07132-6. BMC Genomics. 2020. PMID: 33099302 Free PMC article.
-
Primary orthologs from local sequence context.BMC Bioinformatics. 2020 Feb 6;21(1):48. doi: 10.1186/s12859-020-3384-2. BMC Bioinformatics. 2020. PMID: 32028880 Free PMC article.
-
Origins of variation in the fungal cell surface.Nat Rev Microbiol. 2004 Jul;2(7):533-40. doi: 10.1038/nrmicro927. Nat Rev Microbiol. 2004. PMID: 15197389 Review. No abstract available.
Cited by
-
The Effects of Ivermectin on Brugia malayi Females In Vitro: A Transcriptomic Approach.PLoS Negl Trop Dis. 2016 Aug 16;10(8):e0004929. doi: 10.1371/journal.pntd.0004929. eCollection 2016 Aug. PLoS Negl Trop Dis. 2016. PMID: 27529747 Free PMC article.
-
Reduced selective constraint in endosymbionts: elevation in radical amino acid replacements occurs genome-wide.PLoS One. 2011;6(12):e28905. doi: 10.1371/journal.pone.0028905. Epub 2011 Dec 14. PLoS One. 2011. PMID: 22194947 Free PMC article.
-
Differential Functional Constraints Cause Strain-Level Endemism in Polynucleobacter Populations.mSystems. 2016 May 24;1(3):e00003-16. doi: 10.1128/mSystems.00003-16. eCollection 2016 May-Jun. mSystems. 2016. PMID: 27822527 Free PMC article.
-
Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.Nucleic Acids Res. 2008 Jan;36(Database issue):D787-92. doi: 10.1093/nar/gkm878. Epub 2007 Nov 3. Nucleic Acids Res. 2008. PMID: 17982176 Free PMC article.
-
Universal patterns of purifying selection at noncoding positions in bacteria.Genome Res. 2008 Jan;18(1):148-60. doi: 10.1101/gr.6759507. Epub 2007 Nov 21. Genome Res. 2008. PMID: 18032729 Free PMC article.
Publication types
MeSH terms
Grants and funding
LinkOut - more resources
Full Text Sources
Other Literature Sources
Molecular Biology Databases
Research Materials
