CoChat
Sign Up
Cited by 623Genomics and Phylogenetic StudiesBioinformatics and Genomic NetworksFractal and DNA sequence analysis

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

Open access
Ostlund, G., Schmitt, T., Forslund, K., Kostler, T., Messina, D. N., Roopra, S., Frings, O., Sonnhammer, E. L. L.·2010·Nucleic Acids Research
DOI 10.1093/nar/gkp931PMC PMC2808972
Open this paper in CoChat — free accountOpen PDF

Abstract

The InParanoid project gathers proteomes of completely sequenced eukaryotic species plus Escherichia coli and calculates pairwise ortholog relationships among them. The new release 7.0 of the database has grown by an order of magnitude over the previous version and now includes 100 species and their collective 1.3 million proteins organized into 42.7 million pairwise ortholog groups. The InParanoid algorithm itself has been revised and is now both more specific and sensitive. Based on results from our recent benchmarking of low-complexity filters in homology assignment, a two-pass BLAST approach was developed that makes use of high-precision compositional score matrix adjustment, but avoids the alignment truncation that sometimes follows. We have also updated the InParanoid web site (http://InParanoid.sbc.su.se). Several features have been added, the response times have been improved and the site now sports a new, clearer look. As the number of ortholog databases has grown, it has become difficult to compare among these resources due to a lack of standardized source data and incompatible representations of ortholog relationships. To facilitate data exchange and comparisons among ortholog databases, we have developed and are making available two XML schemas: SeqXML for the input sequences and OrthoXML for the output ortholog clusters.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1093/nar/gkp931

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • 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 [7]

    The Updates to algorithm section says InParanoid uses BLAST scores for homology detection, but it does not say that higher-scoring sequence pairs are likely to have diverged more recently than lower-scoring pairs. Searches for score rankings, evolutionary distance, and recent divergence found no passage establishing that premise. The section instead cautions that some high-scoring fragment matches do not reflect a common origin for the proteins as a whole. (LLM, conf=0.72)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 35

  1. [1]Fitch WM Distinguishing homologous from analogous proteins Syst. Zool. 1970 19 99 113 5449325
  2. [2]Sonnhammer ELL Koonin EV Orthology, paralogy and proposed classification for paralog subtypes Trends Genet. 2002 18 619 620 12446146
  3. [3]Alexeyenko A Lindberg J Perez-Bercoff A Sonnhammer ELL Overview and comparison of ortholog databases Drug Discov. Today Tech. 2006 3 137 143 24980400
  4. [4]Hulsen T Huynen MA de Vlieg J Groenen PM Benchmarking ortholog identification methods using functional genomics data Genome Biol. 2006 7 R31 16613613 PMC1557999
  5. [5]Dolinski K Botstein D Orthology and functional conservation in eukaryotes Annu. Rev. Genet. 2007 41 465 507 17678444
  6. [6]Chen F Mackey AJ Vermunt JK Roos DS Assessing performance of orthology detection strategies applied to eukaryotic genomes PLoS ONE 2007 2 e383 17440619 PMC1849888
  7. [7]Gabaldón T Large-scale assignment of orthology: back to phylogenetics? Genome Biol. 2008 9 235 18983710 PMC2760865
  8. [8]Kuzniar A van Ham RC Pongor S Leunissen JA The quest for orthologs: finding the corresponding gene across genomes Trends Genet. 2008 24 539 551 18819722
  9. [9]Altenhoff AM Dessimoz C Phylogenetic and functional assessment of orthologs inference projects and methods PLoS Comp. Biol. 2009 5 e1000262 PMC2612752 19148271
  10. [10]Hubbard TJ Aken BL Ayling S Ballester B Beal K Bragin E Brent S Chen Y Clapham P Clarke L Ensembl 2009 Nucleic Acids Res. 2009 37 D690 D697 19033362 PMC2686571
  11. [11]Tweedie S Ashburner M Falls K Leyland P McQuilton P Marygold S Millburn G Osumi-Sutherland D Schroeder A Seal R FlyBase Consortium FlyBase: enhancing Drosophila Gene Ontology annotations Nucleic Acids Res. 2009 37 D555 D559 18948289 PMC2686450
  12. [12]Pruitt KD Tatusova T Maglott DR NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins Nucleic Acids Res. 2007 35 D61 65 17130148 PMC1716718
  13. [13]Bieri T Blasiar D Ozersky P Antoshechkin I Bastiani C Canaran P Chan J Chen N Chen WJ Davis P WormBase: new content and better access Nucleic Acids Res. 2007 35 D506 D510 17099234 PMC1669750
  14. [15]Lawson D Arensburger P Atkinson P Besansky NJ Bruggner RV Butler R Campbell KS Christophides GK Christley S Dialynas E VectorBase: a home for invertebrate vectors of human pathogens Nucleic Acids Res. 2007 35 D503 D505 17145709 PMC1751530
  15. [16]Aurrecoechea C Brestelli J Brunk BP Dommer J Fischer S Gajria B Gao X Gingle A Grant G Harb OS PlasmoDB: a functional genomic database for malaria parasites Nucleic Acids Res. 2009 37 D539 D543 18957442 PMC2686598
  16. [17]Heiges M Wang H Robinson E Aurrecoechea C Gao X Kaluskar N Rhodes P Wang S He CZ Su Y CryptoDB: a Cryptosporidium bioinformatics resource update Nucleic Acids Res. 2006 34 D419 D422 16381902 PMC1347441
  17. [18]Aurrecoechea C Brestelli J Brunk BP Carlton JM Dommer J Fischer S Gajria B Gao X Gingle A Grant G GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis Nucleic Acids Res. 2009 37 D526 D530 18824479 PMC2686445
  18. [19]Mi H Guo N Kejariwal A Thomas PD PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways Nucleic Acids Res. 2007 35 D247 D252 17130144 PMC1716723
  19. [20]Ouyang S Zhu W Hamilton J Lin H Campbell M Childs K Thibaud-Nissen F Malek RL Lee Y Zheng L The TIGR Rice Genome Annotation Resource: improvements and new features Nucleic Acids Res. 2007 35 D883 D887 17145706 PMC1751532
  20. [21]Fey P Gaudet P Curk T Zupan B Just EM Basu S Merchant SN Bushmanova YA Shaulsky G Kibbe WA DictyBase–a Dictyostelium bioinformatics resource update Nucleic Acids Res. 2009 37 D515 D519 18974179 PMC2686522
  21. [22]Arnaud MB Costanzo MC Skrzypek MS Shah P Binkley G Lane C Miyasato SR Sherlock G Sequence resources at the Candida Genome Database (CGD) Nucleic Acids Res. 2007 35 D452 D456 17090582 PMC1669745
  22. [23]Wang J Xia Q He X Dai M Ruan J Chen J Yu G Yuan H Hu Y Li R SilkDB: a knowledgebase for silkworm biology and genomics Nucleic Acids Res. 2005 33 D399 D402 15608225 PMC540070
  23. [24]Hong EL Balakrishnan R Dong Q Christie KR Park J Binkley G Costanzo MC Dwight SS Engel SR Fisk DG Gene Ontology annotations at SGD: new data sources and annotation methods Nucleic Acids Res. 2008 36 D577 D581 17982175 PMC2238894
  24. [26]Swarbreck D Wilks C Lamesch P Berardini TZ Garcia-Hernandez M Foerster H Li D Meyer T Muller R Ploetz L The Arabidopsis Information Resource (TAIR): gene structure and function annotation Nucleic Acids Res. 2008 36 D1009 D1014 17986450 PMC2238962
  25. [27]Forslund K Sonnhammer ELL Benchmarking homology detection procedures with low complexity filters Bioinformatics 2009 25 2500 2505 19620098
  26. [28]Altschul SF Wootton JC Gertz EM Agarwala R Morgulis A Schäffer AA Yu YK Protein database searches using compositionally adjusted substitution matrices FEBS J. 2005 272 5101 5109 16218944 PMC1343503
  27. [29]Yu YK Altschul SF The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions Bioinformatics 2005 21 902 911 15509610
  28. [31]The Reference Genome Group of the Gene Ontology Consortium The Gene Ontology's; Reference Genome Project: a unified framework for functional annotation across species PLoS Comput. Biol. 2009 5 e1000431 19578431 PMC2699109
  29. [32]Lassmann T Frings O Sonnhammer ELL Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features Nucleic Acids Res. 2009 37 858 865 19103665 PMC2647288
  30. [33]Sonnhammer ELL Hollich V Scoredist: a simple and robust protein sequence distance estimator BMC Bioinformatics 2005 6 108 15857510 PMC1131889
  31. [34]Berglund AC Sjölund E Östlund G Sonnhammer ELL InParanoid 6: eukaryotic ortholog clusters with inparalogs Nucleic Acids Res 2008 36 D263 D266 18055500 PMC2238924
  32. [35]Vanacova S Liston DR Tachezy J Johnson PJ Molecular biology of the amitochondriate parasites, Giardia intestinalis, Entamoeba histolytica and Trichomonas vaginalis Int. J. Parasitol. 2003 33 235 255 12670510
  33. [36]Xu P Widmer G Wang Y Ozaki LS Alves JM Serrano MG Puiu D Manque P Akiyoshi D Mackey AJ The genome of Cryptosporidium hominis Nature 2008 431 1107 1112 15510150
  34. [37]Lassmann T Sonnhammer ELL Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment Nucleic Acids Res. 2006 34 W596 W599 16845078 PMC1538774
  35. [38]Zmasek CM Eddy SR ATV: display and manipulation of annotated phylogenetic trees Bioinformatics 2001 17 383 384 11301314

Cited by

Sorted by citations

Authors
Ostlund, G., Schmitt, T., Forslund, K., Kostler, T., Messina, D. N., Roopra, S., Frings, O., & Sonnhammer, E. L. L.
Affiliations
  • Stockholm University (SE)
  • AlbaNova (SE)
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2009-11-05
Volume
38
Issue
Database
Pages
D196-D203
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkp931
PMC
PMC2808972
OpenAlex
W2082202339
Cited by
623
References
1
Citations by year
2026: 4 · 2025: 9 · 2024: 9 · 2023: 9 · 2022: 17 · 2021: 27 · 2020: 30 · 2019: 26 · 2018: 27 · 2017: 47 · 2016: 49 · 2015: 61 · 2014: 78 · 2013: 98 · 2012: 66
FWCI
16.25
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • MDC Repository (Max-Delbrueck-Center for Molecular Medicine) (acceptedVersion)
  • KTH Publication Database DiVA (KTH Royal Institute of Technology) (submittedVersion, other-oa)
  • HighWire Press Open Archive (submittedVersion)
Funders
Vetenskapsrådet
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
InParanoid, orthogroups, eukaryotic proteomes, BLAST, low-complexity filters, XML Schema, Escherichia coli
MeSH terms
Algorithms, Animals, Escherichia coli, Eukaryotic Cells, Humans, Proteins, Software, Cluster Analysis, Information Storage and Retrieval, Genome, Bacterial, Protein Structure, Tertiary, Computational Biology, Internet, Databases, Genetic, Databases, Nucleic Acid, Proteomics

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review