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Results: 1 to 20 of 108

1.

Bellman's GAP--a language and compiler for dynamic programming in sequence analysis.

Sauthoff G, Möhl M, Janssen S, Giegerich R.

Bioinformatics. 2013 Mar 1;29(5):551-60. doi: 10.1093/bioinformatics/btt022. Epub 2013 Jan 25.

PMID:
23355290
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Versatile and declarative dynamic programming using pair algebras.

Steffen P, Giegerich R.

BMC Bioinformatics. 2005 Sep 12;6:224. Erratum in: BMC Bioinformatics. 2006;7:214.

PMID:
16156887
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

HMMoC--a compiler for hidden Markov models.

Lunter G.

Bioinformatics. 2007 Sep 15;23(18):2485-7. Epub 2007 Jul 10.

PMID:
17623703
[PubMed - indexed for MEDLINE]
Free Article
4.

A comparison of common programming languages used in bioinformatics.

Fourment M, Gillings MR.

BMC Bioinformatics. 2008 Feb 5;9:82. doi: 10.1186/1471-2105-9-82.

PMID:
18251993
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Design and implementation of a domain specific language for phylogenetic inference.

Pontelli E, Ranjan D, Gupta G, Milligan B.

J Bioinform Comput Biol. 2003 Jul;1(2):201-30.

PMID:
15290770
[PubMed - indexed for MEDLINE]
6.

Automated programming for bioinformatics algorithm deployment.

Alterovitz G, Jiwaji A, Ramoni MF.

Bioinformatics. 2008 Feb 1;24(3):450-1. doi: 10.1093/bioinformatics/btm602. Epub 2008 Jan 3.

PMID:
18174185
[PubMed - indexed for MEDLINE]
Free Article
7.

pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows.

Reeder J, Steffen P, Giegerich R.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W320-4. Epub 2007 May 3.

PMID:
17478505
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

A systematic approach to dynamic programming in bioinformatics.

Giegerich R.

Bioinformatics. 2000 Aug;16(8):665-77. Review.

PMID:
11099253
[PubMed - indexed for MEDLINE]
Free Article
9.

SeqAn an efficient, generic C++ library for sequence analysis.

Döring A, Weese D, Rausch T, Reinert K.

BMC Bioinformatics. 2008 Jan 9;9:11. doi: 10.1186/1471-2105-9-11.

PMID:
18184432
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

GLAD: a system for developing and deploying large-scale bioinformatics grid.

Teo YM, Wang X, Ng YK.

Bioinformatics. 2005 Mar;21(6):794-802. Epub 2004 Sep 23.

PMID:
15388517
[PubMed - indexed for MEDLINE]
Free Article
11.

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.

PMID:
20472540
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

RNA Movies 2: sequential animation of RNA secondary structures.

Kaiser A, Krüger J, Evers DJ.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W330-4. Epub 2007 Jun 12.

PMID:
17567618
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

BioRuby: bioinformatics software for the Ruby programming language.

Goto N, Prins P, Nakao M, Bonnal R, Aerts J, Katayama T.

Bioinformatics. 2010 Oct 15;26(20):2617-9. doi: 10.1093/bioinformatics/btq475. Epub 2010 Aug 25.

PMID:
20739307
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

The Bioinformatics Template Library--generic components for biocomputing.

Pitt WR, Williams MA, Steven M, Sweeney B, Bleasby AJ, Moss DS.

Bioinformatics. 2001 Aug;17(8):729-37.

PMID:
11524374
[PubMed - indexed for MEDLINE]
Free Article
15.

DCA: an efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment.

Stoye J, Moulton V, Dress AW.

Comput Appl Biosci. 1997 Dec;13(6):625-6.

PMID:
9475994
[PubMed - indexed for MEDLINE]
16.

BioJava: an open-source framework for bioinformatics.

Holland RC, Down TA, Pocock M, Prlić A, Huen D, James K, Foisy S, Dräger A, Yates A, Heuer M, Schreiber MJ.

Bioinformatics. 2008 Sep 15;24(18):2096-7. doi: 10.1093/bioinformatics/btn397. Epub 2008 Aug 8.

PMID:
18689808
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

MolBioLib: a C++11 framework for rapid development and deployment of bioinformatics tasks.

Ohsumi TK, Borowsky ML.

Bioinformatics. 2012 Oct 1;28(19):2412-6. Epub 2012 Jul 19.

PMID:
22815363
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Biotool2Web: creating simple Web interfaces for bioinformatics applications.

Shahid M, Alam I, Fuellen G.

Appl Bioinformatics. 2006;5(1):63-6.

PMID:
16539540
[PubMed - indexed for MEDLINE]
19.

Object-oriented sequence analysis: SCL--a C++ class library.

Vahrson W, Hermann K, Kleffe J, Wittig B.

Comput Appl Biosci. 1996 Apr;12(2):119-27.

PMID:
8744774
[PubMed - indexed for MEDLINE]
20.

Locomotif: from graphical motif description to RNA motif search.

Reeder J, Reeder J, Giegerich R.

Bioinformatics. 2007 Jul 1;23(13):i392-400.

PMID:
17646322
[PubMed - indexed for MEDLINE]
Free Article

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