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Items: 1 to 20 of 123

1.

Genome-wide synteny through highly sensitive sequence alignment: Satsuma.

Grabherr MG, Russell P, Meyer M, Mauceli E, Alföldi J, Di Palma F, Lindblad-Toh K.

Bioinformatics. 2010 May 1;26(9):1145-51. doi: 10.1093/bioinformatics/btq102. Epub 2010 Mar 5.

2.
3.

Accurate anchoring alignment of divergent sequences.

Huang W, Umbach DM, Li L.

Bioinformatics. 2006 Jan 1;22(1):29-34. Epub 2005 Nov 13.

PMID:
16301203
4.

Accurate identification of orthologous segments among multiple genomes.

Hachiya T, Osana Y, Popendorf K, Sakakibara Y.

Bioinformatics. 2009 Apr 1;25(7):853-60. doi: 10.1093/bioinformatics/btp070. Epub 2009 Feb 2. Erratum in: Bioinformatics. 2009 Jun 1;25(11):1474.

PMID:
19188192
5.

Specific alignment of structured RNA: stochastic grammars and sequence annealing.

Bradley RK, Pachter L, Holmes I.

Bioinformatics. 2008 Dec 1;24(23):2677-83. doi: 10.1093/bioinformatics/btn495. Epub 2008 Sep 16.

6.

Transposable element annotation of the rice genome.

Juretic N, Bureau TE, Bruskiewich RM.

Bioinformatics. 2004 Jan 22;20(2):155-60.

PMID:
14734305
7.

GATA: a graphic alignment tool for comparative sequence analysis.

Nix DA, Eisen MB.

BMC Bioinformatics. 2005 Jan 17;6:9.

8.

Interactive software tool to comprehend the calculation of optimal sequence alignments with dynamic programming.

Ibarra IL, Melo F.

Bioinformatics. 2010 Jul 1;26(13):1664-5. doi: 10.1093/bioinformatics/btq252. Epub 2010 May 14.

9.

Genome comparison without alignment using shortest unique substrings.

Haubold B, Pierstorff N, Möller F, Wiehe T.

BMC Bioinformatics. 2005 May 23;6:123.

10.

Fast algorithms for large-scale genome alignment and comparison.

Delcher AL, Phillippy A, Carlton J, Salzberg SL.

Nucleic Acids Res. 2002 Jun 1;30(11):2478-83.

11.

OpenStructure: an integrated software framework for computational structural biology.

Biasini M, Schmidt T, Bienert S, Mariani V, Studer G, Haas J, Johner N, Schenk AD, Philippsen A, Schwede T.

Acta Crystallogr D Biol Crystallogr. 2013 May;69(Pt 5):701-9. doi: 10.1107/S0907444913007051. Epub 2013 Apr 19.

12.

Fast and accurate short read alignment with Burrows-Wheeler transform.

Li H, Durbin R.

Bioinformatics. 2009 Jul 15;25(14):1754-60. doi: 10.1093/bioinformatics/btp324. Epub 2009 May 18.

13.

BEAST: Bayesian evolutionary analysis by sampling trees.

Drummond AJ, Rambaut A.

BMC Evol Biol. 2007 Nov 8;7:214.

14.

Simultaneous alignment of short reads against multiple genomes.

Schneeberger K, Hagmann J, Ossowski S, Warthmann N, Gesing S, Kohlbacher O, Weigel D.

Genome Biol. 2009;10(9):R98. doi: 10.1186/gb-2009-10-9-r98. Epub 2009 Sep 17.

15.

BLAT--the BLAST-like alignment tool.

Kent WJ.

Genome Res. 2002 Apr;12(4):656-64.

16.

Fast model-based protein homology detection without alignment.

Hochreiter S, Heusel M, Obermayer K.

Bioinformatics. 2007 Jul 15;23(14):1728-36. Epub 2007 May 8.

PMID:
17488755
17.

SeSAW: balancing sequence and structural information in protein functional mapping.

Standley DM, Yamashita R, Kinjo AR, Toh H, Nakamura H.

Bioinformatics. 2010 May 1;26(9):1258-9. doi: 10.1093/bioinformatics/btq116. Epub 2010 Mar 17.

18.

Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis.

Yavatkar AS, Lin Y, Ross J, Fann Y, Brody T, Odenwald WF.

BMC Genomics. 2008 Feb 28;9:106. doi: 10.1186/1471-2164-9-106.

19.

JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow.

Latorre M, Silva H, Saba J, Guziolowski C, Vizoso P, Martinez V, Maldonado J, Morales A, Caroca R, Cambiazo V, Campos-Vargas R, Gonzalez M, Orellana A, Retamales J, Meisel LA.

BMC Bioinformatics. 2006 Nov 23;7:513.

20.

MODBASE, a database of annotated comparative protein structure models, and associated resources.

Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, Webb B, Greenblatt D, Huang CC, Ferrin TE, Sali A.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D217-22.

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