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Tag genefinding [56 articles]

Recent papers classified by the tag genefinding.
  • A practical guide to the art of RNA gene prediction
    Brief Bioinform (4 May 2007), bbm011.
    by Irmtraud M Meyer
    posted to rna methods geneprediction genefinding by tharris on 2008-06-20 17:01:02 as ** along with 5 people xingxu penka wenhan GustavoLacerda xili03
  • Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species
    BMC Bioinformatics, Vol. 9 (13 June 2008), 278.
    by Oliver Keller, Florian Odronitz, Mario Stanke, Martin Kollmar, Stephan Waack
    posted to genomics geneprediction genefinding by tharris on 2008-06-20 16:53:40 as ** along with 1 person GustavoLacerda
  • Finding genes in Plasmodium falciparum.
    Nature, Vol. 404, No. 6773. (2 March 2000)
    by M Pertea, SL Salzberg, MJ Gardner
    posted to computational falciparum genefinding by mdimon on 2007-10-15 21:25:45 as ** along with 1 person shung
  • Prediction of complete gene structures in human genomic DNA.
    J Mol Biol, Vol. 268, No. 1. (25 April 1997), pp. 78-94.
    by C Burge, S Karlin
    posted to genefinding hmm human plant vertebrate by kaspermunch on 2005-11-22 08:48:39 as read along with 9 people and 2 groups bandrewfox nklee pcahan1 indigoviolet dullhunk dquest wenhan GustavoLacerda nicholso Bioinformatics EisenLab
  • Automatic generation of gene finders for eukaryotic species
    BMC Bioinformatics, Vol. 7, No. 1. (2006)
    by Kasper Munch, Anders Krogh
    posted to genefinding by kaspermunch on 2007-09-11 21:21:25 as ** along with 2 people and 1 group alexl GustavoLacerda Bioinformatics
  • Microbial gene identification using interpolated Markov models.
    Nucleic Acids Res, Vol. 26, No. 2. (15 January 1998), pp. 544-548.
    by SL Salzberg, AL Delcher, S Kasif, O White
    posted to genefinding hmm markov by jguinney on 2006-09-04 15:45:58 as *** along with 5 people and 1 group wenhan ziquje gg bnchakraborty bluto MBLAB
  • Improving gene recognition accuracy by combining predictions from two gene-finding programs
    Bioinformatics, Vol. 18, No. 8. (1 August 2002), pp. 1034-1045.
    by Sanja Rogic, Francis BF Ouellette, Alan K Mackworth
    posted to genefinding by GustavoLacerda on 2008-01-22 18:25:41 as ** along with 1 person and 1 group indigoviolet EisenLab
  • Computer programs for eukaryotic gene prediction
    Brief Bioinform, Vol. 3, No. 2. (1 January 2002), pp. 195-199.
    by Vladimir Makarov
    posted to genefinding by GustavoLacerda on 2007-04-19 23:03:19 as **
  • prot4EST: Translating Expressed Sequence Tags from neglected genomes
    BMC Bioinformatics, Vol. 5, No. 1. (2004)
    by James Wasmuth, Mark Blaxter
    posted to est genefinding by GustavoLacerda on 2008-03-18 17:41:40 as **
  • An evaluation of contemporary hidden Markov model genefinders with a predicted exon taxonomy
    Nucleic Acids Research, Vol. 35, No. 1. (January 2007), pp. 317-324.
    by Knapp, Keith, Chen, Yi-Ping Phoebe
    posted to genefinding by GustavoLacerda on 2007-05-08 17:02:59 as ** along with 2 people and 1 group indigoviolet wenhan EisenLab
  • Hypothesis testing approaches to the exon prediction problem
    Bioinformatics, Vol. 22, No. 24. (15 December 2006), pp. 3003-3008.
    by Vilardell, Mireia, Sanchez-Pla, Alex
    posted to genefinding by GustavoLacerda on 2007-05-09 21:26:42 as **
  • The presence of GC-AG introns in Neurospora crassa and other euascomycetes determined from analyses of complete genomes: implications for automated gene prediction
    Genomics, Vol. 87, No. 3. (March 2006), pp. 338-347.
    by Martijn Rep, Roselinde G Duyvesteijn, Liane Gale, Thomas Usgaard, Ben J Cornelissen, Li-Jun Ma, Todd J Ward
    posted to fungi genefinding splicing by GustavoLacerda on 2007-06-06 19:38:56 as **
  • CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction
    Genome Biology, Vol. 8 (20 December 2007), R269.
    by Samuel S Gross, Chuong B Do, Marina Sirota, Serafim Batzoglou
    posted to genefinding by GustavoLacerda on 2008-01-07 14:51:24 as ** along with 2 people and 2 groups stajich renatomilani EisenLab Berkeley Mycology
  • Homology search for genes
    Bioinformatics, Vol. 23, No. 13. (1 July 2007), pp. i97-103.
    by Xuefeng Cui, Tomas Vinar, Brona Brejova, Dennis Shasha, Ming Li
    posted to genefinding by GustavoLacerda on 2007-07-25 17:52:17 as ** along with 1 person jyuh
  • Current methods of gene prediction, their strengths and weaknesses.
    Nucleic Acids Res, Vol. 30, No. 19. (1 October 2002), pp. 4103-4117.
    by C Mathé, MF Sagot, T Schiex, P Rouzé
    posted to genefinding by GustavoLacerda on 2007-05-09 20:51:59 as ** along with 3 people wenhan ep161302 arcticrasta
  • Computational approaches to gene prediction.
    J Microbiol, Vol. 44, No. 2. (April 2006), pp. 137-144.
    by JH Do, DK Choi
    posted to genefinding by GustavoLacerda on 2007-05-02 19:18:09 as ** along with 1 person and 1 group indigoviolet EisenLab
  • Advancing the State of the Art in Computational Gene Prediction
    Knowledge Discovery and Emergent Complexity in Bioinformatics (2007), pp. 81-106.
    by William Majoros, Uwe Ohler
    posted to genefinding by GustavoLacerda on 2008-01-21 12:40:23 as **
  • Intron length distributions and gene prediction
    Nucl. Acids Res. (7 July 2007), gkm281.
    by Scott W Roy, David Penny
    posted to genefinding splicing by GustavoLacerda on 2007-08-03 20:21:48 as ** along with 2 people cabbagezs Jporci
  • Predicting essential genes in fungal genomes
    Genome Res., Vol. 16, No. 9. (1 September 2006), pp. 1126-1135.
    by Michael Seringhaus, Alberto Paccanaro, Anthony Borneman, Michael Snyder, Mark Gerstein
    posted to genefinding by GustavoLacerda on 2007-05-09 21:24:48 as ** along with 4 people balicea saket olympos dbenn
  • A method of precise mRNA/DNA homology-based gene structure prediction.
    BMC Bioinformatics, Vol. 6 (21 October 2005)
    by A Churbanov, M Pauley, D Quest, H Ali
    posted to genefinding by GustavoLacerda on 2007-04-28 00:59:43 as *** along with 1 person jwortman
  • Heuristic approach to deriving models for gene finding.
    Nucleic Acids Res, Vol. 27, No. 19. (1 October 1999), pp. 3911-3920.
    by J Besemer, M Borodovsky
    posted to genefinding by GustavoLacerda on 2008-07-09 04:27:04 as ** along with 4 people and 2 groups alexl azazello indigoviolet wenhan MBLAB EisenLab
  • Comparative analysis of sequence features involved in the recognition of tandem splice sites
    BMC Genomics, Vol. 9 (30 April 2008), 202.
    by Ralf Bortfeldt, Stefanie Schindler, Karol Szafranski, Stefan Schuster, Dirk Holste
    posted to splicing genefinding by GustavoLacerda on 2008-05-05 17:59:25 as **
  • Computational prediction of eukaryotic protein-coding genes.
    Nat Rev Genet, Vol. 3, No. 9. (September 2002), pp. 698-709.
    by MQ Zhang
    posted to genefinding by GustavoLacerda on 2007-05-02 19:10:21 as ** along with 3 people and 3 groups wenhan indigoviolet dchughes EisenLab G4ID Genetics-of-Gambling
  • Steady progress and recent breakthroughs in the accuracy of automated genome annotation
    Nat Rev Genet, Vol. 9, No. 1. (January 2008), pp. 62-73.
    by Michael R Brent
    posted to genefinding by GustavoLacerda on 2008-07-14 15:44:31 as ** along with 7 people alexl jyuh dchughes jermth wenhan renatomilani drbal
  • CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes
    Bioinformatics, Vol. 23, No. 9. (1 May 2007), pp. 1061-1067.
    by Genis Parra, Keith Bradnam, Ian Korf
    posted to genefinding by GustavoLacerda on 2007-08-21 22:46:03 as ** along with 3 people and 2 groups indigoviolet stajich wenhan EisenLab Berkeley Mycology
  • In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists
    Bioinformatics, Vol. 23, No. 4. (15 February 2007), pp. 414-420.
    by Saeys, Yvan, Rouze, Pierre, Van de Peer, Yves
    posted to genefinding by GustavoLacerda on 2007-05-09 20:44:14 as ** along with 1 person wenhan
  • EuSplice: A unified resource for the analysis of splice signals and alternative splicing in eukaryotic genes.
    Bioinformatics (7 March 2007)
    by Ashwini Bhasi, Ram Vinay V Pandey, Suriya Prabha P Utharasamy, Periannan Senapathy
    posted to genefinding splicing by GustavoLacerda on 2007-10-27 05:48:11 as ** along with 1 person jyuh
  • PALMA: mRNA to genome alignments using large margin algorithms
    Bioinformatics, Vol. 23, No. 15. (1 August 2007), pp. 1892-1900.
    by Uta Schulze, Bettina Hepp, Cheng S Ong, Gunnar Ratsch
    posted to est2genome genefinding by GustavoLacerda on 2007-08-17 17:45:20 as ** along with 1 person cjeans
  • Characterization and prediction of alternative splice sites
    Gene, Vol. 366, No. 2. (1 February 2006), pp. 219-227.
    by Magnus Wang, Antonio Marin
    posted to genefinding splicing by GustavoLacerda on 2007-10-27 05:42:38 as ** along with 1 person and 2 groups dchughes G4ID Genetics-of-Gambling
  • Gene prediction and verification in a compact genome with numerous small introns
    Genome Res., Vol. 14, No. 11. (1 November 2004), pp. 2330-2335.
    by Aaron E Tenney, Randall H Brown, Charles Vaske, Jennifer K Lodge, Tamara L Doering, Michael R Brent
    posted to fungi genefinding by GustavoLacerda on 2007-05-09 20:06:47 as **
  • Finding exonic islands in a sea of non-coding sequence: splicing related constraints on protein composition and evolution are common in intron-rich genomes
    Genome Biology, Vol. 9, No. 2. (2008)
    by Tobias Warnecke, Joanna Parmley, Laurence Hurst
    posted to genefinding splicing by GustavoLacerda on 2008-03-04 14:05:49 as ** along with 1 person biomcgary
  • Computational Inference of Homologous Gene Structures in the Human Genome
    Genome Res., Vol. 11, No. 5. (1 May 2001), pp. 803-816.
    by Ru-Fang Yeh, Lee P Lim, Christopher B Burge
    posted to genefinding by GustavoLacerda on 2007-07-19 01:39:50 as ** along with 1 person and 1 group indigoviolet EisenLab
  • Gene finding in novel genomes.
    BMC Bioinformatics, Vol. 5 (14 May 2004)
    by I Korf
    posted to genefinding by GustavoLacerda on 2007-05-02 19:45:06 as ** along with 5 people and 1 group alexl LeightonP indigoviolet wenhan cmzmasek EisenLab
  • Coevolution of genomic intron number and splice sites.
    Trends Genet, Vol. 23, No. 7. (July 2007), pp. 321-325.
    by M Irimia, D Penny, SW Roy
    posted to genefinding by GustavoLacerda on 2007-10-27 05:21:21 as ** along with 4 people and 1 group dpollard stajich Manchester seitentaisei EisenLab
  • Global Discriminative Learning for Higher-Accuracy Computational Gene Prediction
    PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e54.
    by Axel Bernal, Koby Crammer, Artemis Hatzigeorgiou, Fernando Pereira
    posted to genefinding by GustavoLacerda on 2007-08-18 05:46:22 as ** along with 1 person and 1 group dpollard EisenLab
  • GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005)
    by J Besemer, M Borodovsky
    posted to genefinding by GustavoLacerda on 2008-01-23 23:23:35 as ** along with 2 people jmeppley wenhan
  • An analysis of gene-finding programs for Neurospora crassa
    Bioinformatics, Vol. 17, No. 10. (1 October 2001), pp. 901-912.
    by Eileen Kraemer, Jian Wang, Jinhua Guo, Samuel Hopkins, Jonathan Arnold
    posted to genefinding by GustavoLacerda on 2007-05-04 20:38:50 as **
  • MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes
    Genome Res. (19 November 2007), gr.6743907.
    by Brandi L Cantarel, Ian Korf, Sofia M Robb, Genis Parra, Eric Ross, Barry Moore, Carson Holt, Sanchez, Mark Yandell
    posted to genefinding by GustavoLacerda on 2008-01-23 23:22:03 as ** along with 5 people jamselem tharris timflutre stajich urgi
  • Introns and splicing elements of five diverse fungi.
    Eukaryot Cell, Vol. 3, No. 5. (October 2004), pp. 1088-1100.
    by DM Kupfer, SD Drabenstot, KL Buchanan, H Lai, H Zhu, DW Dyer, BA Roe, JW Murphy
    posted to fungi genefinding splicing by GustavoLacerda on 2007-05-04 18:50:04 as ** along with 5 people and 2 groups penka jwestbrook alexl angieju seitentaisei Nie King_Lab
  • FlyBase: genes and gene models.
    Nucleic Acids Res, Vol. 33, No. Database issue. (1 January 2005)
    by RA Drysdale, MA Crosby,
    posted to genefinding genome by GustavoLacerda on 2007-11-19 18:48:56 as ** along with 2 people dragonrez nuke2005
  • Positive selection for unpreferred codon usage in eukaryotic genomes
    BMC Evolutionary Biology, Vol. 7 (18 July 2007), 119.
    by Daniel E Neafsey, James E Galagan
    posted to genefinding genomics by GustavoLacerda on 2007-07-27 20:12:37 as ** along with 1 person Ema
  • Incorporation of splice site probability models for non-canonical introns improves gene structure prediction in plants.
    Bioinformatics, Vol. 21 Suppl 3 (1 November 2005)
    by ME Sparks, V Brendel
    posted to genefinding splicing by GustavoLacerda on 2007-06-12 02:03:38 as **
  • Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
    Genome Biology, Vol. 9 (11 January 2008), R7.
    by Brian J Haas, Steven L Salzberg, Wei Zhu, Mihaela Pertea, Jonathan E Allen, Joshua Orvis, Owen R White, Robin C Buell, Jennifer R Wortman
    posted to genefinding by GustavoLacerda on 2008-01-18 19:10:27 as ** along with 2 people and 1 group stajich mclarenv Berkeley Mycology
  • TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders
    Bioinformatics, Vol. 20, No. 16. (1 November 2004), pp. 2878-2879.
    by WH Majoros, M Pertea, SL Salzberg
    posted to genefinding by GustavoLacerda on 2007-05-02 19:37:51 as ** along with 2 people and 1 group alexl indigoviolet EisenLab
  • Prediction of splice sites with dependency graphs and their expanded bayesian networks
    Bioinformatics, Vol. 21, No. 4. (15 February 2005), pp. 471-482.
    by Te-Ming Chen, Chung-Chin Lu, Wen-Hsiung Li
    posted to genefinding splicing by GustavoLacerda on 2007-06-08 15:32:47 as **
  • Contemporary Progress in Gene Structure Prediction
    Current Genomics, Vol. 7, No. 5. (August 2006), pp. 283-292.
    by Churbanov, Alexander
    posted to genefinding by GustavoLacerda on 2007-06-12 01:58:42 as **
  • ANGLE: a sequencing errors resistant program for predicting protein coding regions in unfinished cDNA.
    J Bioinform Comput Biol, Vol. 4, No. 3. (June 2006), pp. 649-664.
    by K Shimizu, J Adachi, Y Muraoka
    posted to est genefinding by GustavoLacerda on 2007-07-18 21:30:50 as **
  • Gene identification in novel eukaryotic genomes by self-training algorithm
    Nucleic Acids Research, Vol. 33, No. 20. (2005), pp. 6494-6506.
    by Alexandre Lomsadze, Vardges Ter-Hovhannisyan, Yury O Chernoff, Mark Borodovsky
    posted to genefinding by GustavoLacerda on 2007-05-02 19:35:25 as ** along with 1 person wenhan
  • Getting Started in Probabilistic Graphical Models
    PLoS Computational Biology, Vol. 3, No. 12. (1 December 2007), e252.
    by Edoardo M Airoldi
    posted to genefinding graphical_models by GustavoLacerda on 2008-01-22 17:36:25 as ** along with 12 people and 1 group jfr jyuh balicea AbnerCYH stajich cjeans GeeSharpMinor sobolevnrm cabbagezs nklee biehl softsimu baker-group
  • Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources
    BMC Bioinformatics, Vol. 7, No. 1. (2006)
    by Mario Stanke, Oliver Schoffmann, Burkhard Morgenstern, Stephan Waack
    posted to genefinding by GustavoLacerda on 2007-04-18 17:25:04 as ** along with 3 people and 1 group alexl azazello wenhan MBLAB
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