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Items: 1 to 20 of 90


Effective cluster-based seed design for cross-species sequence comparisons.

Zhou L, Mihai I, Florea L.

Bioinformatics. 2008 Dec 15;24(24):2926-7. doi: 10.1093/bioinformatics/btn547. Epub 2008 Oct 20.


Universal seeds for cDNA-to-genome comparison.

Zhou L, Stanton J, Florea L.

BMC Bioinformatics. 2008 Jan 23;9:36. doi: 10.1186/1471-2105-9-36.


Comparative annotation of viral genomes with non-conserved gene structure.

de Groot S, Mailund T, Hein J.

Bioinformatics. 2007 May 1;23(9):1080-9. Epub 2007 Mar 6.


Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison.

Brown CT, Xie Y, Davidson EH, Cameron RA.

BMC Bioinformatics. 2005 Mar 24;6:70.


Efficient filtering methods for clustering cDNAs with spliced sequence alignment.

Shibuya T, Kashima H, Konagaya A.

Bioinformatics. 2004 Jan 1;20(1):29-39.


Efficient combination of multiple word models for improved sequence comparison.

Huang X, Ye L, Chou HH, Yang IH, Chao KM.

Bioinformatics. 2004 Nov 1;20(16):2529-33. Epub 2004 Apr 29.


Murasaki: a fast, parallelizable algorithm to find anchors from multiple genomes.

Popendorf K, Tsuyoshi H, Osana Y, Sakakibara Y.

PLoS One. 2010 Sep 24;5(9):e12651. doi: 10.1371/journal.pone.0012651.


PSAT: a web tool to compare genomic neighborhoods of multiple prokaryotic genomes.

Fong C, Rohmer L, Radey M, Wasnick M, Brittnacher MJ.

BMC Bioinformatics. 2008 Mar 26;9:170. doi: 10.1186/1471-2105-9-170.


Efficient multiple genome alignment.

Höhl M, Kurtz S, Ohlebusch E.

Bioinformatics. 2002;18 Suppl 1:S312-20.


Automatic clustering of orthologs and inparalogs shared by multiple proteomes.

Alexeyenko A, Tamas I, Liu G, Sonnhammer EL.

Bioinformatics. 2006 Jul 15;22(14):e9-15.


Efficient estimation of pairwise distances between genomes.

Domazet-Loso M, Haubold B.

Bioinformatics. 2009 Dec 15;25(24):3221-7. doi: 10.1093/bioinformatics/btp590. Epub 2009 Oct 13.


SEED: efficient clustering of next-generation sequences.

Bao E, Jiang T, Kaloshian I, Girke T.

Bioinformatics. 2011 Sep 15;27(18):2502-9. doi: 10.1093/bioinformatics/btr447. Epub 2011 Aug 2.


Adaptive seeds tame genomic sequence comparison.

Kiełbasa SM, Wan R, Sato K, Horton P, Frith MC.

Genome Res. 2011 Mar;21(3):487-93. doi: 10.1101/gr.113985.110. Epub 2011 Jan 5.


Multiseed lossless filtration.

Kucherov G, Noé L, Roytberg M.

IEEE/ACM Trans Comput Biol Bioinform. 2005 Jan-Mar;2(1):51-61.


Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus.

Brendel V, Xing L, Zhu W.

Bioinformatics. 2004 May 1;20(7):1157-69. Epub 2004 Feb 5.


WindowMasker: window-based masker for sequenced genomes.

Morgulis A, Gertz EM, Schäffer AA, Agarwala R.

Bioinformatics. 2006 Jan 15;22(2):134-41. Epub 2005 Nov 15.


Scipio: using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species.

Keller O, Odronitz F, Stanke M, Kollmar M, Waack S.

BMC Bioinformatics. 2008 Jun 13;9:278. doi: 10.1186/1471-2105-9-278.


ClutrFree: cluster tree visualization and interpretation.

Bidaut G, Ochs MF.

Bioinformatics. 2004 Nov 1;20(16):2869-71. Epub 2004 May 14.


Rainbow: a toolbox for phylogenetic supertree construction and analysis.

Chen D, Eulenstein O, Fernández-Baca D.

Bioinformatics. 2004 Nov 1;20(16):2872-3. Epub 2004 May 14.

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