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Items: 1 to 20 of 74


Orthology detection combining clustering and synteny for very large datasets.

Lechner M, Hernandez-Rosales M, Doerr D, Wieseke N, Thévenin A, Stoye J, Hartmann RK, Prohaska SJ, Stadler PF.

PLoS One. 2014 Aug 19;9(8):e105015. doi: 10.1371/journal.pone.0105015. eCollection 2014.


Proteinortho: detection of (co-)orthologs in large-scale analysis.

Lechner M, Findeiss S, Steiner L, Marz M, Stadler PF, Prohaska SJ.

BMC Bioinformatics. 2011 Apr 28;12:124. doi: 10.1186/1471-2105-12-124.


SyntTax: a web server linking synteny to prokaryotic taxonomy.

Oberto J.

BMC Bioinformatics. 2013 Jan 16;14:4. doi: 10.1186/1471-2105-14-4.


Orthology and paralogy constraints: satisfiability and consistency.

Lafond M, El-Mabrouk N.

BMC Genomics. 2014;15 Suppl 6:S12. doi: 10.1186/1471-2164-15-S6-S12. Epub 2014 Oct 17.


Breaking the computational barriers of pairwise genome comparison.

Torreno O, Trelles O.

BMC Bioinformatics. 2015 Aug 11;16:250. doi: 10.1186/s12859-015-0679-9.


Screening synteny blocks in pairwise genome comparisons through integer programming.

Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M.

BMC Bioinformatics. 2011 Apr 18;12:102. doi: 10.1186/1471-2105-12-102.


Identification of mammalian orthologs using local synteny.

Jun J, Mandoiu II, Nelson CE.

BMC Genomics. 2009 Dec 23;10:630. doi: 10.1186/1471-2164-10-630.


Identification of genomic features using microsyntenies of domains: domain teams.

Pasek S, Bergeron A, Risler JL, Louis A, Ollivier E, Raffinot M.

Genome Res. 2005 Jun;15(6):867-74. Epub 2005 May 17.


The gene family-free median of three.

Doerr D, Balaban M, Feijão P, Chauve C.

Algorithms Mol Biol. 2017 May 26;12:14. doi: 10.1186/s13015-017-0106-z. eCollection 2017.


Identifying gene clusters by discovering common intervals in indeterminate strings.

Doerr D, Stoye J, Böcker S, Jahn K.

BMC Genomics. 2014;15 Suppl 6:S2. doi: 10.1186/1471-2164-15-S6-S2. Epub 2014 Oct 17.


Quantitative synteny scoring improves homology inference and partitioning of gene families.

Ali RH, Muhammad S, Khan M, Arvestad L.

BMC Bioinformatics. 2013;14 Suppl 15:S12. doi: 10.1186/1471-2105-14-S15-S12. Epub 2013 Oct 15.


A modified hyperplane clustering algorithm allows for efficient and accurate clustering of extremely large datasets.

Sharma A, Podolsky R, Zhao J, McIndoe RA.

Bioinformatics. 2009 May 1;25(9):1152-7. doi: 10.1093/bioinformatics/btp123. Epub 2009 Mar 4.


The evolution of protostome GATA factors: molecular phylogenetics, synteny, and intron/exon structure reveal orthologous relationships.

Gillis WQ, Bowerman BA, Schneider SQ.

BMC Evol Biol. 2008 Apr 15;8:112. doi: 10.1186/1471-2148-8-112.


Domain similarity based orthology detection.

Bitard-Feildel T, Kemena C, Greenwood JM, Bornberg-Bauer E.

BMC Bioinformatics. 2015 May 13;16:154. doi: 10.1186/s12859-015-0570-8.


Absynte: a web tool to analyze the evolution of orthologous archaeal and bacterial gene clusters.

Despalins A, Marsit S, Oberto J.

Bioinformatics. 2011 Oct 15;27(20):2905-6. doi: 10.1093/bioinformatics/btr473. Epub 2011 Aug 11.


SynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes.

Drillon G, Carbone A, Fischer G.

PLoS One. 2014 Mar 20;9(3):e92621. doi: 10.1371/journal.pone.0092621. eCollection 2014.


Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing.

Wittkop T, Baumbach J, Lobo FP, Rahmann S.

BMC Bioinformatics. 2007 Oct 17;8:396.


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