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FACIL: Fast and Accurate Genetic Code Inference and Logo.

Dutilh BE, Jurgelenaite R, Szklarczyk R, van Hijum SA, Harhangi HR, Schmid M, de Wild B, Françoijs KJ, Stunnenberg HG, Strous M, Jetten MS, Op den Camp HJ, Huynen MA.

Bioinformatics. 2011 Jul 15;27(14):1929-33. doi: 10.1093/bioinformatics/btr316. Epub 2011 Jun 8.


Genetic code prediction for metazoan mitochondria with GenDecoder.

Abascal F, Zardoya R, Posada D.

Methods Mol Biol. 2009;537:233-42. doi: 10.1007/978-1-59745-251-9_11.


TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences.

Teeling H, Waldmann J, Lombardot T, Bauer M, Glöckner FO.

BMC Bioinformatics. 2004 Oct 26;5:163.


MRS: a fast and compact retrieval system for biological data.

Hekkelman ML, Vriend G.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W766-9.


Optimality of the genetic code with respect to protein stability and amino-acid frequencies.

Gilis D, Massar S, Cerf NJ, Rooman M.

Genome Biol. 2001;2(11):RESEARCH0049. Epub 2001 Oct 24.


GenDecoder: genetic code prediction for metazoan mitochondria.

Abascal F, Zardoya R, Posada D.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W389-93.


BatchPrimer3: a high throughput web application for PCR and sequencing primer design.

You FM, Huo N, Gu YQ, Luo MC, Ma Y, Hane D, Lazo GR, Dvorak J, Anderson OD.

BMC Bioinformatics. 2008 May 29;9:253. doi: 10.1186/1471-2105-9-253.


A new web-based data mining tool for the identification of candidate genes for human genetic disorders.

van Driel MA, Cuelenaere K, Kemmeren PP, Leunissen JA, Brunner HG.

Eur J Hum Genet. 2003 Jan;11(1):57-63.


Pattern locator: a new tool for finding local sequence patterns in genomic DNA sequences.

Mrázek J, Xie S.

Bioinformatics. 2006 Dec 15;22(24):3099-100. Epub 2006 Nov 8.


PDA: a pipeline to explore and estimate polymorphism in large DNA databases.

Casillas S, Barbadilla A.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W166-9.


PanCGHweb: a web tool for genotype calling in pangenome CGH data.

Bayjanov JR, Siezen RJ, van Hijum SA.

Bioinformatics. 2010 May 1;26(9):1256-7. doi: 10.1093/bioinformatics/btq103. Epub 2010 Mar 10.


TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations.

Abascal F, Zardoya R, Telford MJ.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W7-13. doi: 10.1093/nar/gkq291. Epub 2010 Apr 30.


DNAlive: a tool for the physical analysis of DNA at the genomic scale.

Goñi JR, Fenollosa C, Pérez A, Torrents D, Orozco M.

Bioinformatics. 2008 Aug 1;24(15):1731-2. doi: 10.1093/bioinformatics/btn259. Epub 2008 Jun 9.


GENSTYLE: exploration and analysis of DNA sequences with genomic signature.

Fertil B, Massin M, Lespinats S, Devic C, Dumee P, Giron A.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W512-5.


Genomic BLAST: custom-defined virtual databases for complete and unfinished genomes.

Cummings L, Riley L, Black L, Souvorov A, Resenchuk S, Dondoshansky I, Tatusova T.

FEMS Microbiol Lett. 2002 Nov 5;216(2):133-8.


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.


WebLogo: a sequence logo generator.

Crooks GE, Hon G, Chandonia JM, Brenner SE.

Genome Res. 2004 Jun;14(6):1188-90.

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