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di indigoviolet algorithm [97 articles]

Articoli aggiunti di recente alla biblioteca di indigoviolet classificati sotto il tag algorithm. You can also see everyone's algorithm.
  • Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
    Bioinformatics, Vol. 15, No. 7. (1 July 1999), pp. 563-577.
    by Gz Hertz, Gd Stormo
    posted to algorithm motif by indigoviolet on 2007-12-12 14:01:38 as ** along with 4 people and 1 group tuck dquest lusk chad_davis EisenLab
  • Combining evidence using p-values: application to sequence homology searches.
    Bioinformatics, Vol. 14, No. 1. (1998), pp. 48-54.
    by TL Bailey, M Gribskov
    posted to algorithm by indigoviolet on 2007-12-12 10:57:32 as ** along with 1 person and 1 group sconlan EisenLab
  • Statistical extraction of Drosophila cis-regulatory modules using exhaustive assessment of local word frequency.
    BMC Bioinformatics, Vol. 4 (22 December 2003)
    by AG Nazina, DA Papatsenko
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-12 09:21:45 as ** along with 1 group EisenLab
  • Detection of cis -element clusters in higher eukaryotic DNA
    Bioinformatics, Vol. 17, No. 10. (1 October 2001), pp. 878-889.
    by Martin C Frith, Ulla Hansen, Zhiping Weng
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-12 09:15:36 as ** along with 1 group EisenLab
  • Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences
    Nucl. Acids Res., Vol. 30, No. 14. (15 July 2002), pp. 3214-3224.
    by Martin C Frith, John L Spouge, Ulla Hansen, Zhiping Weng
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-12 09:15:32 as ** along with 1 person and 1 group xili03 EisenLab
  • ClusterDraw web server: a tool to identify and visualize clusters of binding motifs for transcription factors
    Bioinformatics, Vol. 23, No. 8. (15 April 2007), pp. 1032-1034.
    by Papatsenko, Dmitri
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-12 09:12:26 as ** along with 1 person and 1 group jyuh EisenLab
  • Cluster-Buster: finding dense clusters of motifs in DNA sequences
    Nucl. Acids Res., Vol. 31, No. 13. (1 July 2003), pp. 3666-3668.
    by Martin C Frith, Michael C Li, Zhiping Weng
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-12 09:10:09 as ** along with 1 group EisenLab
  • Decoding human regulatory circuits.
    Genome Res, Vol. 14, No. 10A. (October 2004), pp. 1967-1974.
    by W Thompson, MJ Palumbo, WW Wasserman, JS Liu, CE Lawrence
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-12 09:09:40 as ** along with 1 person and 1 group chad_davis EisenLab
  • CisModule: de novo discovery of cis-regulatory modules by hierarchical mixture modeling.
    Proc Natl Acad Sci U S A, Vol. 101, No. 33. (17 August 2004), pp. 12114-12119.
    by Q Zhou, WH Wong
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-12 08:38:23 as ** along with 2 people and 1 group dpollard ep161302 EisenLab
  • De novo cis-regulatory module elicitation for eukaryotic genomes
    PNAS, Vol. 102, No. 20. (17 May 2005), pp. 7079-7084.
    by Mayetri Gupta, Jun S Liu
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-12 08:37:52 as ** along with 3 people and 1 group tuck lusk ihpark EisenLab
  • Modulefinder: a tool for computational discovery of cis regulatory modules.
    Pac Symp Biocomput (2005), pp. 519-530.
    by AA Philippakis, FS He, ML Bulyk
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-12 07:50:58 as ** along with 1 person and 1 group ccr EisenLab
  • Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm.
    Bioinformatics, Vol. 19 Suppl 1 (2003)
    by O Johansson, W Alkema, WW Wasserman, J Lagergren
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-12 07:47:27 as ** along with 2 people and 1 group xili03 isimpson EisenLab
  • MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes.
    BMC Bioinformatics, Vol. 6 (2005)
    by VD Marinescu, IS Kohane, A Riva
    posted to algorithm motif by indigoviolet on 2007-12-12 05:44:21 as ** along with 1 person and 1 group ihpark EisenLab
  • CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments.
    Bioinformatics, Vol. 19 Suppl 1 (2003)
    by R Sharan, I Ovcharenko, A Ben-Hur, RM Karp
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-12 05:41:45 as ** along with 1 person and 1 group dquest EisenLab
  • Identification of regulatory regions which confer muscle-specific gene expression
    Journal of Molecular Biology, Vol. 278, No. 1. (24 April 1998), pp. 167-181.
    by Wyeth W Wasserman, James W Fickett
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-12 05:40:08 as ** along with 2 people and 1 group gpalidwor isimpson EisenLab
  • Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura.
    Bioinformatics, Vol. 20, No. 16. (1 November 2004), pp. 2738-2750.
    by YH Grad, FP Roth, MS Halfon, GM Church
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-11 10:22:44 as ** along with 1 person and 1 group maximilianh EisenLab
  • Finding cis-regulatory modules in Drosophila using phylogenetic hidden Markov models
    Bioinformatics, Vol. 23, No. 16. (15 August 2007), pp. 2031-2037.
    by Wendy S Wong, Rasmus Nielsen
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-11 05:05:47 as ** along with 2 people and 1 group cabbagezs csdhwang EisenLab
  • Searching for statistically significant regulatory modules.
    Bioinformatics, Vol. 19 Suppl 2 (October 2003)
    by TL Bailey, WS Noble
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-05 13:00:37 as ** along with 2 people and 2 groups stajich xili03 EisenLab Berkeley Mycology
  • Homotypic regulatory clusters in Drosophila.
    Genome Res, Vol. 13, No. 4. (April 2003), pp. 579-588.
    by AP Lifanov, VJ Makeev, AG Nazina, DA Papatsenko
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-05 12:56:45 as ** along with 1 person and 1 group tresch EisenLab
  • Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo.
    Proc Natl Acad Sci U S A, Vol. 99, No. 2. (22 January 2002), pp. 763-768.
    by M Markstein, P Markstein, V Markstein, MS Levine
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-05 12:38:23 as ** along with 1 person and 1 group dpollard EisenLab
  • SCORE: A computational approach to the identification of cis-regulatory modules and target genes in whole-genome sequence data
    Proceedings of the National Academy of Sciences, Vol. 99, No. 15. (23 July 2002), pp. 9888-9893.
    by Mark Rebeiz, Nick L Reeves, James W Posakony
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-05 12:37:56 as ** along with 2 people and 1 group isimpson GustavoLacerda EisenLab
  • Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA
    Bioinformatics, Vol. 22, No. 23. (1 December 2006), pp. 2858-2864.
    by Pierstorff, Nora, Bergman, M Casey, Wiehe, Thomas
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-05 12:15:18 as ** along with 2 people and 1 group brant emilyhare EisenLab
  • Stubb: a program for discovery and analysis of cis-regulatory modules.
    Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006)
    by S Sinha, Y Liang, E Siggia
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-05 12:14:38 as ** along with 2 people and 1 group Stew csdhwang EisenLab
  • Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila.
    BMC Bioinformatics, Vol. 5 (9 September 2004)
    by S Sinha, MD Schroeder, U Unnerstall, U Gaul, ED Siggia
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-05 12:14:10 as ** along with 1 group EisenLab
  • Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo.
    BMC Bioinformatics, Vol. 3 (24 October 2002)
    by N Rajewsky, M Vergassola, U Gaul, ED Siggia
    posted to algorithm enhancer-prediction by indigoviolet on 2007-12-05 12:13:43 as ** along with 5 people and 1 group ansobol adepace koller Stew csdhwang EisenLab
  • BLAT--the BLAST-like alignment tool.
    Genome Res, Vol. 12, No. 4. (April 2002), pp. 656-664.
    by WJ Kent
    posted to algorithm alignment by indigoviolet on 2007-12-03 20:27:15 as ** along with 18 people and 1 group operon miguel pcahan1 Ayest mtagaya treangen michC djkt timflutre olympos cjeans wenhan natstreet antonkratz yoanjacquemin talponer bozdagd gpappas EisenLab
  • PAML: a program package for phylogenetic analysis by maximum likelihood.
    Comput Appl Biosci, Vol. 13, No. 5. (October 1997), pp. 555-556.
    by Z Yang
    posted to algorithm molecular-evolution by indigoviolet on 2007-12-03 18:07:12 as ** along with 11 people and 3 groups bjorns chrn chad_davis penka BioNica stajich pv usagi-kirin jmjimenez tharris skumagai EisenLab Nie Berkeley Mycology
  • T-Coffee: A novel method for fast and accurate multiple sequence alignment.
    J Mol Biol, Vol. 302, No. 1. (8 September 2000), pp. 205-217.
    by C Notredame, DG Higgins, J Heringa
    posted to algorithm alignment by indigoviolet on 2007-12-03 18:04:40 as ** along with 9 people and 1 group miguel dayjm ffranca treangen Haggan siebertm adijr marti newton1234 EisenLab
  • Whole-genome sequence assembly for mammalian genomes: Arachne 2.
    Genome Res, Vol. 13, No. 1. (January 2003), pp. 91-96.
    by DB Jaffe, J Butler, S Gnerre, E Mauceli, K Lindblad-Toh, JP Mesirov, MC Zody, ES Lander
    posted to algorithm assembly by indigoviolet on 2007-12-03 12:32:59 as ** along with 4 people and 1 group bpb AaronDarling wenhan farhat EisenLab
  • Base-calling of automated sequencer traces using phred. II. Error probabilities.
    Genome Res, Vol. 8, No. 3. (March 1998), pp. 186-194.
    by B Ewing, P Green
    posted to algorithm by indigoviolet on 2007-12-03 12:32:33 as ** along with 3 people and 2 groups balajis giovanni bozdagd Bioinformatics EisenLab
  • Aligning multiple genomic sequences with the threaded blockset aligner.
    Genome Res, Vol. 14, No. 4. (April 2004), pp. 708-715.
    by M Blanchette, WJ Kent, C Riemer, L Elnitski, AF Smit, KM Roskin, R Baertsch, K Rosenbloom, H Clawson, ED Green, D Haussler, W Miller
    posted to algorithm alignment by indigoviolet on 2007-12-03 12:28:07 as ** along with 8 people and 1 group operon ujh csardas djkt yylin Neeperando maralena AlexanderPico EisenLab
  • AVID: A Global Alignment Program
    Genome Res., Vol. 13, No. 1. (1 January 2003), pp. 97-102.
    by Nick Bray, Inna Dubchak, Lior Pachter
    posted to algorithm alignment by indigoviolet on 2007-12-03 12:24:41 as ** along with 2 people and 1 group adijr yoanjacquemin EisenLab
  • DIALIGN: finding local similarities by multiple sequence alignment
    Bioinformatics, Vol. 14, No. 3. (1 April 1998), pp. 290-294.
    by B Morgenstern, K Frech, A Dress, T Werner
    posted to algorithm alignment by indigoviolet on 2007-12-03 12:11:49 as ** along with 1 person and 1 group adijr EisenLab
  • Human-Mouse Alignments with BLASTZ
    Genome Res., Vol. 13, No. 1. (1 January 2003), pp. 103-107.
    by Scott Schwartz, James W Kent, Arian Smit, Zheng Zhang, Robert Baertsch, Ross C Hardison, David Haussler, Webb Miller
    posted to algorithm alignment by indigoviolet on 2007-12-03 12:10:51 as ** along with 3 people and 1 group operon treangen nedwards EisenLab
  • Benchmarking tools for the alignment of functional noncoding DNA.
    BMC Bioinformatics, Vol. 5 (21 January 2004)
    by DA Pollard, CM Bergman, J Stoye, SE Celniker, MB Eisen
    posted to algorithm alignment evaluation by indigoviolet on 2007-12-03 12:09:57 as ** along with 5 people and 1 group lilou adijr idonaldson gjuggler nklee EisenLab
  • GeneComber: combining outputs of gene prediction programs for improved results
    Bioinformatics, Vol. 19, No. 10. (1 July 2003), pp. 1296-1297.
    by Sohrab P Shah, Graham P Mcvicker, Alan K Mackworth, Sanja Rogic, Francis BF Ouellette
    posted to algorithm gene-prediction by indigoviolet on 2007-12-03 11:44:07 as ** along with 1 group EisenLab
  • Pairagon+N-SCAN_EST: a model-based gene annotation pipeline.
    Genome Biol, Vol. 7 Suppl 1 (2006)
    by M Arumugam, C Wei, RH Brown, MR Brent
    posted to algorithm gene-prediction by indigoviolet on 2007-12-03 10:46:38 as ** along with 1 person and 1 group wenhan EisenLab
  • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
    Nucleic Acids Res, Vol. 25, No. 17. (1 September 1997), pp. 3389-3402.
    by SF Altschul, TL Madden, AA Schäffer, J Zhang, Z Zhang, W Miller, DJ Lipman
    posted to algorithm alignment by indigoviolet on 2007-12-03 10:41:36 as ** along with 45 people and 4 groups dakelley knaseanka setar iakes miguel kaarsinogen bjorns bicko jmeppley chad_davis balajis nuke2005 eweaver david_parsons dullhunk robert dgront happy_manatee caporaso treangen kengg manzanita leelarcombe CitoJam jdelcampo aengisch rabio massivemayhem mirzazadeh azazello sujaikumar beatrizfernandez GustavoLacerda siebertm adijr viktor21614 mijam grottenolm bandrewfox edvin newton1234 mariakmejia granujilla marti CharlesM EisenLab biomedical-nlp Microbial-Ecology Plantandetc
  • Identification of protein coding regions by database similarity search.
    Nat Genet, Vol. 3, No. 3. (March 1993), pp. 266-272.
    by W Gish, DJ States
    posted to algorithm alignment computational by indigoviolet on 2007-12-03 10:39:38 as ** along with 2 people and 1 group bluto wenhan EisenLab
  • CONTRAST: de novo gene prediction using a semi-Markov conditional random field. Biomedical Computation at Stanford Symposium Proceedings (BCATS)
    (2005)
    by SS Gross, CB Do, S Batzoglou
    posted to algorithm gene-prediction by indigoviolet on 2007-12-03 10:27:25 as **
  • Gene finding with a hidden Markov model of genome structure and evolution.
    Bioinformatics, Vol. 19, No. 2. (22 January 2003), pp. 219-227.
    by JS Pedersen, J Hein
    posted to algorithm gene-prediction by indigoviolet on 2007-12-03 10:24:55 as ** along with 3 people and 2 groups redelings stajich azazello EisenLab MBLAB
  • Untitled
    posted to algorithm gene-prediction by indigoviolet on 2007-12-03 10:20:44 as **
  • The conserved exon method for gene finding.
    Proc Int Conf Intell Syst Mol Biol, Vol. 8 (2000), pp. 3-12.
    by V Bafna, DH Huson
    posted to algorithm gene-prediction by indigoviolet on 2007-12-03 10:02:41 as ** along with 1 person and 2 groups wenhan EisenLab MBLAB
  • Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction
    Genome Res., Vol. 10, No. 7. (1 July 2000), pp. 950-958.
    by Serafim Batzoglou, Lior Pachter, Jill P Mesirov, Bonnie Berger, Eric S Lander
    posted to algorithm gene-prediction by indigoviolet on 2007-12-03 10:01:18 as ** along with 3 people and 2 groups j3xucite treangen wenhan EisenLab MBLAB
  • Comparative ab initio prediction of gene structures using pair HMMs.
    Bioinformatics, Vol. 18, No. 10. (October 2002), pp. 1309-1318.
    by IM Meyer, R Durbin
    posted to algorithm gene-prediction by indigoviolet on 2007-12-03 09:58:55 as ** along with 3 people and 2 groups azazello acarbo wenhan EisenLab MBLAB
  • SLAM web server for comparative gene finding and alignment.
    Nucleic Acids Res, Vol. 31, No. 13. (1 July 2003), pp. 3507-3509.
    by S Cawley, L Pachter, M Alexandersson
    posted to algorithm gene-prediction by indigoviolet on 2007-12-03 09:57:13 as ** along with 1 group EisenLab
  • SGP-1: prediction and validation of homologous genes based on sequence alignments.
    Genome Res, Vol. 11, No. 9. (September 2001), pp. 1574-1583.
    by T Wiehe, S Gebauer-Jung, T Mitchell-Olds, R Guigó
    posted to algorithm gene-prediction by indigoviolet on 2007-12-03 09:56:29 as ** along with 1 person and 1 group wenhan EisenLab
  • Gene recognition via spliced sequence alignment.
    Proc Natl Acad Sci U S A, Vol. 93, No. 17. (20 August 1996), pp. 9061-9066.
    by MS Gelfand, AA Mironov, PA Pevzner
    posted to algorithm gene-prediction by indigoviolet on 2007-12-03 09:53:35 as ** along with 1 person and 1 group wenhan EisenLab
  • GeneMark.hmm: new solutions for gene finding.
    Nucleic Acids Res, Vol. 26, No. 4. (15 February 1998), pp. 1107-1115.
    by AV Lukashin, M Borodovsky
    posted to algorithm gene-prediction by indigoviolet on 2007-12-03 09:52:55 as ** along with 1 person and 1 group wenhan EisenLab
  • Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach.
    Proc Natl Acad Sci U S A, Vol. 88, No. 24. (15 December 1991), pp. 11261-11265.
    by EC Uberbacher, RJ Mural
    posted to algorithm gene-prediction by indigoviolet on 2007-12-03 07:20:03 as ** along with 1 group EisenLab
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