CoChat
Sign Up
Cited by 14Genomics and Phylogenetic StudiesGenome Rearrangement AlgorithmsChromosomal and Genetic Variations

SynBlast: Assisting the analysis of conserved synteny information

Open access
Lehmann, Jörg, Stadler, Peter F, Prohaska, Sonja J·2008·BMC Bioinformatics
DOI 10.1186/1471-2105-9-351PMC PMC2543028
Open this paper in CoChat — free accountOpen PDF

Abstract

MOTIVATION: In the last years more than 20 vertebrate genomes have been sequenced, and the rate at which genomic DNA information becomes available is rapidly accelerating. Gene duplication and gene loss events inherently limit the accuracy of orthology detection based on sequence similarity alone. Fully automated methods for orthology annotation do exist but often fail to identify individual members in cases of large gene families, or to distinguish missing data from traceable gene losses. This situation can be improved in many cases by including conserved synteny information. RESULTS: Here we present the SynBlast pipeline that is designed to construct and evaluate local synteny information. SynBlast uses the genomic region around a focal reference gene to retrieve candidates for homologous regions from a collection of target genomes and ranks them in accord with the available evidence for homology. The pipeline is intended as a tool to aid high quality manual annotation in particular in those cases where automatic procedures fail. We demonstrate how SynBlast is applied to retrieving orthologous and paralogous clusters using the vertebrate Hox and ParaHox clusters as examples. SOFTWARE: The SynBlast package written in Perl is available under the GNU General Public License at http://www.bioinf.uni-leipzig.de/Software/SynBlast/.

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 · 10.1186/1471-2105-9-351

Cites

2 of 2 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?

  • Orthologous chains tend to cover several genes located in a conserved order, resulting in higher synteny values, which can help distinguish orthologs from paralogs.

    “Orthologous chains tend to cover several genes located in a conserved order, resulting in higher synteny values, which can help to distinguish orthologs from paralogs (14, 41–43).”

    From Integrating gene annotation with orthology inference at scale (2023) · cites this paper as [41]

    The Background defines conserved synteny as maintenance of gene content and order, and the Results (Algorithms and Implementation; page unavailable) say gene-order scores help distinguish putative orthologous from paralogous regions. The paper does not establish that orthologous chains generally span several genes or have higher synteny values than paralogous chains. (LLM, conf=0.78)

    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: 41

  1. Pevzner P Tesler G Genome rearrangements in mammalian evolution: lessons from human and mouse genomes Genome Res 2003 13 37 45 12529304 PMC430962
  2. Boffelli D Nobrega MA Rubin EM Comparative genomics at the vertebrate extremes Nat Rev Genet 2004 5 456 465 15153998
  3. Ma J Zhang L Suh BB Raney BJ Burhans RC Kent WJ Blanchette M Haussler D Miller W Reconstructing contiguous regions of an ancestral genome Genome Res 2006 16 1557 1565 16983148 PMC1665639
  4. Kikuta H Laplante M Navratilova P Komisarczuk AZ Engström PG Fredman D Akalin A Caccamo M Sealy I Howe K Ghislain J Pezeron G Mourrain P Ellingsen S Oates AC Thisse C Thisse B Foucher I Adolf B Geling A Lenhard B Becker TS Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates Genome Res 2007 17 545 555 17387144 PMC1855176
  5. Wagner GP Takahashi K Lynch V Prohaska SJ Fried C Stadler PF Amemiya CT Molecular Evolution of Duplicated Ray Finned Fish HoxA Clusters: Increased synonymous substitution rate and asymmetrical co-divergence of coding and non-coding sequences J Mol Evol 2005 665 676 15983874
  6. Remm M Storm CE Sonnhammer EL Automatic clustering of orthologs and in-paralogs from pairwise species comparisons J Mol Biol 2001 314 1041 1052 11743721
  7. O'Brien KP Remm M Sonnhammer ELL Inparanoid: a comprehensive database of eukaryotic orthologs Nucleic Acids Res 2005 33 D476 D480 15608241 PMC540061
  8. Berglund AC Sjölund E Ostlund G Sonnhammer ELL InParanoid 6: eukaryotic ortholog clusters with inparalogs Nucleic Acids Res 2008 36 D263 D266 18055500 PMC2238924
  9. Kamvysselis M Patterson N Birren B Berger B Lander ES Vingron M, Istrail S, Pevzner P, Waterman WM, Miller Whole-genome comparative annotation and regulatory motif discovery in multiple yeast species Proceedings of the seventh annual international conference on Research in computational molecular biology 2003 ACM 157 166
  10. Flicek P Aken BL Beal K Ballester B Caccamo M Chen Y Clarke L Coates G Cunningham F Cutts T Down T Dyer SC Eyre T Fitzgerald S Fernandez-Banet J Gräf S Haider S Hammond M Holland R Howe KL Howe K Johnson N Jenkinson A Kähäri A Keefe D Kokocinski F Kulesha E Lawson D Longden I Megy K Meidl P Overduin B Parker A Pritchard B Prlic A Rice S Rios D Schuster M Sealy I Slater G Smedley D Spudich G Trevanion S Vilella AJ Vogel J White S Wood M Birney E Cox T Curwen V Durbin R Fernandez-Suarez XM Herrero J Hubbard TJP Kasprzyk A Proctor G Smith J Ureta-Vidal A Searle S Ensembl 2008 Nucleic Acids Res 2008 36 D707 D714 18000006 PMC2238821
  11. Goodstadt L Ponting CP Phylogenetic Reconstruction of Orthology, Paralogy, and Conserved Synteny for Dog and Human PLoS Comput Biol 2006 2 e133 17009864 PMC1584324
  12. Zheng XH Lu F Wang ZY Zhong F Hoover J Mural R Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs Bioinformatics 2005 21 703 710 15458983
  13. Vandepoele K Saeys Y Simillion C Raes J Peer Y Van De The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice Genome Res 2002 12 1792 1801 12421767 PMC187543
  14. Haas BJ Delcher AL Wortman JR Salzberg SL DAGchainer: A tool for mining segmental genome duplications and synteny Bioinformatics 2004 20 3643 3646 15247098
  15. Soderlund C Nelson W Shoemaker A Paterson A SyMAP: A system for discovering and viewing syntenic regions of FPC maps Genome Res 2006 16 1159 1168 16951135 PMC1557773
  16. Choi V Zheng C Zhu Q Sankoff D Algorithms for the Extraction of Synteny Blocks from Comparative Maps WABI: Algorithms in Bioinformatics, 7th International Workshop, Volume 4645 of Lecture Notes in Computer Science 2007 Heidelberg: Springer 277 288
  17. Kriventseva EV Rahman N Espinosa O Zdobnov EM OrthoDB: the hierarchical catalog of eukaryotic orthologs Nucleic Acids Res 2007 36 D271 D75 17947323 PMC2238902
  18. Altschul SF Madden TL Schäffer AA Zhang J Zhang Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res 1997 25 3389 3402 9254694 PMC146917
  19. Kent WJ BLAT-the BLAST-like alignment tool Genome Res 2002 12 656 664 11932250 PMC187518
  20. Fried C Hordijk W Prohaska SJ Stadler CR Stadler PF The Footprint Sorting Problem J Chem Inf Comput Sci 2004 44 332 338 15032508
  21. Duboule D Dollé P The structural and functional organization of the murine HOX gene family resembles that of Drosophila homeotic genes EMBO J 1989 8 1497 1505 2569969 PMC400980
  22. McGinnis W Krumlauf R Homeobox genes and axial patterning Cell 1992 68 283 302 1346368
  23. Ferrier DEK Holland PWH Ancient Origin of the Hox gene cluster Nat Rev Genet 2001 2 33 38 11253066
  24. Holland PWH Beyond the Hox: How widespread is homeobox gene clustering? J Anatomy 2001 199 13 23 PMC1594991 11523814
  25. Garcia-Fernandez J The genesis and evolution of homeobox gene clusters Nat Rev Genet 2005 6 881 892 16341069
  26. Bailey WJ Kim J Wagner GP Ruddle FH Phylogenetic reconstruction of vertebrate Hox cluster duplications Mol Biol Evol 1997 14 843 853 9254922
  27. Crow KD Stadler PF Lynch VJ Amemiya C Wagner GP The fish-specific Hox cluster duplication is coincident with the origin of teleosts Mol Biol Evol 2006 23 121 136 16162861
  28. Stellwag EJ Hox gene duplications in fish Semin Cell Dev Biol 1999 10 531 540 10597637
  29. Taylor J Braasch I Frickey T Meyer A Peer Y Van De Genome duplication, a trait shared by 22,000 species of ray-finned fish Genome Res 2003 13 382 390 12618368 PMC430266
  30. Prohaska S Stadler PF The Duplication of the Hox Gene Clusters in Teleost Fishes Theory Biosci 2004 123 89 110 18202881
  31. Amores A Suzuki T Yan YL Pomeroy J Singer A Amemiya C Postlethwait J Developmental roles of pufferfish Hox clusters and genome evolution in ray-fin fish Genome Res 2004 14 1 10 14707165 PMC314266
  32. Hoegg S Meyer A Hox clusters as models for vertebrate genome evolution Trends Genet 2005 21 421 424 15967537
  33. Crow KD Stadler PF Lynch VJ Amemiya CT Wagner GP The fish specific Hox cluster duplication is coincident with the origin of teleosts Mol Biol Evol 2006 23 121 136 16162861
  34. Hoegg S Boore JL Kuehl JV Meyer A Comparative phylogenomic analyses of teleost fish Hox gene clusters: lessons from the cichlid fish Astatotilapia burtoni BMC Genomics 2007 8 317 17845724 PMC2080641
  35. Duboule D The rise and fall of Hox gene clusters Development 2007 134 2549 2560 17553908
  36. Woltering JM Durston AJ The zebrafish hoxDb cluster has been reduced to a single microRNA Nat Genet 2006 38 601 602 16736008
  37. Prohaska SJ Stadler PF Evolution of the Vertebrate Parahox Clusters J Exp Zoolog B Mol Dev Evol 2006 306 481 487 16619246
  38. Mulley JF Chiu CH Holland PWH Breakup of a homeobox cluster after genome duplication in teleosts Proc Natl Acad Sci USA 2006 103 10369 10372 16801555 PMC1502464
  39. Siegel N Hoegg S Salzburger W Braasch I Meyer A Comparative genomics of ParaHox clusters of teleost fishes: gene cluster breakup and the retention of gene sets following whole genome duplications BMC Genomics 2007 8 312 17822543 PMC2020491
  40. Boekhorst J Snel B Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties BMC Bioinformatics 2007 8 356 17888146 PMC2048517
  41. Kai W Kikuchi K Fujita M Suetake H Fujiwara A Yoshiura Y Ototake M Venkatesh B Miyaki K Suzuki Y A genetic linkage map for the tiger pufferfish, Takifugu rubripes Genetics 2005 171 227 238 15972462 PMC1456513

Cited by

Sorted by citations

Authors
Lehmann, J., Stadler, P. F., & Prohaska, S. J.
Affiliations
  • Leipzig University (DE)
  • University of Vienna (AT)
Corresponding author
Lehmann, Jörg
ORCID
Venue
BMC Bioinformatics
Publisher
Springer Science and Business Media LLC
Published
2008-08-24
Volume
9
Issue
1
Pages
351-351
ISSN
1471-2105 (ISSN-L)
DOI
10.1186/1471-2105-9-351
PMC
PMC2543028
OpenAlex
W2098300089
Cited by
14
References
2
Citations by year
2023: 1 · 2021: 1 · 2014: 2 · 2013: 5
FWCI
0.63
Type
journal article
Language
en
Open access
Licence
Locations
  • BMC Bioinformatics (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Phaidra (Universität Wien) (submittedVersion, cc-by-nc-nd)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Publikationsdatenbank der Fraunhofer-Gesellschaft (Fraunhofer-Gesellschaft) (submittedVersion, other-oa)
  • Publikation Server (Leipzig University) (submittedVersion)
  • Fraunhofer-Publica (Fraunhofer-Gesellschaft) (submittedVersion)
  • Qucosa (Saxon State and University Library Dresden) (submittedVersion, other-oa)
Funders
Deutsche Forschungsgemeinschaft
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
Keywords
conserved synteny, paralogy, gene duplication, gene loss, homology detection, Hox genes, ParaHox genes, vertebrate genomes, manual annotation
MeSH terms
Algorithms, Base Sequence, Chromosome Mapping, Database Management Systems, Genetic Linkage, Molecular Sequence Data, Software, Information Storage and Retrieval, Sequence Alignment, Sequence Analysis, DNA, Gene Order, Synteny, Databases, Genetic

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