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Cited by 64Genomics and Phylogenetic StudiesBioinformatics and Genomic NetworksFractal and DNA sequence analysis

OrthoInspector: comprehensive orthology analysis and visual exploration

Open access
Linard, Benjamin, Thompson, Julie D, Poch, Olivier, Lecompte, Odile·2011·BMC Bioinformatics
DOI 10.1186/1471-2105-12-11PMC PMC3024942
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Abstract

BACKGROUND: The accurate determination of orthology and inparalogy relationships is essential for comparative sequence analysis, functional gene annotation and evolutionary studies. Various methods have been developed based on either simple blast all-versus-all pairwise comparisons and/or time-consuming phylogenetic tree analyses. RESULTS: We have developed OrthoInspector, a new software system incorporating an original algorithm for the rapid detection of orthology and inparalogy relations between different species. In comparisons with existing methods, OrthoInspector improves detection sensitivity, with a minimal loss of specificity. In addition, several visualization tools have been developed to facilitate in-depth studies based on these predictions. The software has been used to study the orthology/in-paralogy relationships for a large set of 940,855 protein sequences from 59 different eukaryotic species. CONCLUSION: OrthoInspector is a new software system for orthology/paralogy analysis. It is made available as an independent software suite that can be downloaded and installed for local use. Command line querying facilitates the integration of the software in high throughput processing pipelines and a graphical interface provides easy, intuitive access to results for the non-expert.

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  • Heuristic analysis of pairwise sequence similarity scores is based on the premise that higher scoring sequence pairs are likely to have diverged more recently than lower scoring sequence pairs.

    “The central premise underlying their use is that higher scoring sequence pairs are likely to have diverged more recently than lower scoring sequence pairs.”

    From OrthoFinder: phylogenetic orthology inference for comparative genomics (2019) · cites this paper as [13]

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Cited by

Sorted by citations

Authors
Linard, B., Thompson, J. D., Poch, O., & Lecompte, O.
Affiliations
Centre National de la Recherche Scientifique (FR)
Corresponding author
Linard, Benjamin
ORCID
Venue
BMC Bioinformatics
Publisher
Springer Science and Business Media LLC
Published
2011-01-10
Volume
12
Issue
1
Pages
11-11
ISSN
1471-2105 (ISSN-L)
DOI
10.1186/1471-2105-12-11
PMC
PMC3024942
OpenAlex
W2012035190
Cited by
64
References
0
Citations by year
2026: 1 · 2024: 1 · 2023: 2 · 2022: 1 · 2021: 2 · 2020: 3 · 2019: 8 · 2018: 6 · 2017: 5 · 2016: 3 · 2015: 2 · 2014: 5 · 2013: 8 · 2012: 8
FWCI
3.66
Type
journal article
Language
en
Open access
Licence
Locations
  • BMC Bioinformatics (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • HAL (submittedVersion, cc-by)
  • HAL (submittedVersion, other-oa)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • univOAK (4 institutions : Université de Strasbourg, Université de Haute Alsace, INSA Strasbourg, Bibliothèque Nationale et Universitaire de Strasbourg) (submittedVersion, cc-by)
Funders
  • Agence Nationale de la Recherche
  • Institut National de la Santé et de la Recherche Médicale
  • Université de Strasbourg
  • Centre National de la Recherche Scientifique
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
Keywords
orthology, paralogy, protein sequence comparison, comparative genomics, functional gene annotation, eukaryotic proteins, visualization tools, software suite
MeSH terms
Algorithms, Phylogeny, Software, Sequence Analysis, Protein, Proteomics, Molecular Sequence Annotation

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