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Tag alignment [593 articles]

Recent papers classified by the tag alignment.
  • Segment-based multiple sequence alignment
    Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i187-192.
    by Tobias Rausch, Anne-Katrin Emde, David Weese, Andreas Doring, Cedric Notredame, Knut Reinert
    posted to sequence alignment by zwang on 2008-08-11 04:14:42 as ** along with 5 people chad_davis aprasad Ema APRegier djkt
  • Mind the Gaps: Evidence of Bias in Estimates of Multiple Sequence Alignments.
    Mol Biol Evol (20 August 2007)
    by Tanya Golubchik, Michael J J Wise, Simon Easteal, Lars S S Jermiin
    posted to alignment sequence by zwang on 2007-11-07 07:45:42 as ** along with 3 people caseybrown lilou dandaman
  • Recent Evolutions of Multiple Sequence Alignment Algorithms
    PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e123.
    by Cédric Notredame
    posted to algorithm alignment evolution sequence by zwang on 2007-09-01 17:08:49 as ** along with 9 people and 2 groups smbe2008 mdimmic rvosa timflutre stajich cabbagezs groepl yoanjacquemin marti Bioinformatics FAB-lab
  • Alignment Uncertainty and Genomic Analysis
    Science, Vol. 319, No. 5862. (25 January 2008), pp. 473-476.
    by Karen M Wong, Marc A Suchard, John P Huelsenbeck
    posted to alignment genome sequence by zwang on 2008-02-18 11:09:28 as ** along with 25 people and 2 groups jfr bpcusack pradiptaray jdelcampo timflutre gracio adacier jyuh bpb aprasad dayjm dpollard tny djkt cjeans lisa1 cactus biomcgary lilou kinestetika dandaman gjuggler renatomilani mclarenv youdon EisenLab microbiology_nijmegen
  • SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Trees Using a Bayesian MCMC Framework
    PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e149.
    by Irmtraud M Meyer, István Miklós
    posted to alignment bayesian phylogeny rna structure by zwang on 2007-09-13 17:47:28 as **** along with 3 people bertelsen raylim cabbagezs
  • A fast structural multiple alignment method for long RNA sequences
    BMC Bioinformatics, Vol. 9 (23 January 2008), 33.
    by Yasuo Tabei, Hisanori Kiryu, Taishin Kin, Kiyoshi Asai
    posted to alignment rna sequence structure by zwang on 2008-02-24 13:44:59 as ***** along with 1 person mtagaya
  • Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method
    Mol Syst Biol, Vol. 4 (12 February 2008)
    by Lukas Burger, Erik van Nimwegen
    posted to alignment bayesian interaction prediction protein sequence by zwang on 2008-02-17 10:10:43 as **** along with 10 people pansapiens kengg grahamc laughcry biomcgary cabbagezs roys cdeane gjuggler phoenixzxl
  • MORPH: Probabilistic Alignment Combined with Hidden Markov Models of cis-Regulatory Modules
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e216.
    by Saurabh Sinha, Xin He
    posted to alignment hmm modeling module regulatory by zwang on 2007-12-10 04:29:31 as *** along with 7 people and 2 groups ana dpollard cjeans maximilianh hpaces Ema uwe EisenLab cis-regulatory-evolution
  • Biclustering As A Method For RNA Local Multiple Sequence Alignment
    Bioinformatics (6 October 2007), btm485.
    by Shu Wang, Robin R Gutell, Daniel P Miranker
    posted to alignment clustering rna sequence by zwang on 2007-12-10 03:49:41 as ** along with 1 person cjeans
  • Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis
    Science, Vol. 320, No. 5883. (20 June 2008), pp. 1632-1635.
    by Ari Loytynoja, Nick Goldman
    posted to phylogeny evolution alignment by zwang on 2008-06-25 05:44:44 as *** along with 22 people and 3 groups marti nuin emptyhb michaelbarton jlgreen AbnerCYH bpcusack bmaust gulsacan Schmidtc bpb aprasad imtechnology marck ArtemPankin djkt gjuggler hpaces dinnes chad_davis jago phoenixzxl iSEEM Green Lab Khavkin's lab
  • Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments
    Proceedings of the National Academy of Sciences, Vol. 105, No. 14. (8 April 2008), pp. 5441-5446.
    by Lei Xie, Philip E Bourne
    posted to alignment evolution profile sequence structure by zwang on 2008-04-09 03:58:23 as ** along with 1 person and 1 group sobolevnrm baker-group
  • Accuracy of structure-based sequence alignments of automatic methods
    BMC Bioinformatics, Vol. 8 (20 September 2007), 355.
    by Changhoon Kim, Byungkook Lee
    posted to accuracy algorithm alignment sequence structure by zwang on 2007-11-01 07:29:02 as *** along with 3 people rabio dimka chad_davis
  • Multiple protein sequence alignment
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Jimin Pei
    posted to sequence alignment by zwang on 2008-06-16 03:49:58 as ** along with 4 people and 1 group sobolevnrm marck paulschlesinger TOchi baker-group
  • Heads or Tails: A Simple Reliability Check for Multiple Sequence Alignments
    Mol Biol Evol, Vol. 24, No. 6. (1 June 2007), pp. 1380-1383.
    by Giddy Landan, Dan Graur
    posted to alignment reliability sequence by zwang on 2007-06-14 02:10:16 as *** along with 7 people and 1 group aprasad rvosa BioNica stajich cjeans lilou mailund FAB-lab
  • Multiple structural alignment and clustering of RNA sequences.
    Bioinformatics (25 February 2007)
    by Elfar Torarinsson, Jakob H H Havgaard, Jan Gorodkin
    posted to alignment clustering rna structure by zwang on 2007-05-01 06:10:22 as ** along with 7 people and 2 groups marcius eckart_bindewald eweaver ppgardne ilh dunnp zhouyu BioinfoCIPF SGU-CIPF
  • Alignment of protein sequences by their profiles.
    Protein Sci, Vol. 13, No. 4. (April 2004), pp. 1071-1087.
    by MA Marti-Renom, MS Madhusudhan, A Sali
    posted to alignment evolution methods multiple by zmasek on 2006-07-25 20:00:36 as ** along with 2 people and 2 groups granujilla marcius BioinfoCIPF SGU-CIPF
  • Homology-extended sequence alignment
    Nucleic Acids Research, Vol. 33, No. 3. (2005), pp. 816-824.
    by VA Simossis, J Kleinjung, J Heringa
    posted to alignment evolution methods multiple by zmasek on 2006-07-25 19:58:50 as **
  • A comprehensive comparison of multiple sequence alignment programs
    Nucl. Acids Res., Vol. 27, No. 13. (1 July 1999), pp. 2682-2690.
    by Jd Thompson, F Plewniak, O Poch
    posted to alignment evolution methods multiple sequence by zmasek on 2006-07-27 04:02:42 as ** along with 1 person treangen
  • Evaluation of iterative alignment algorithms for multiple alignment
    Bioinformatics, Vol. 21, No. 8. (15 April 2005), pp. 1408-1414.
    by Iain M Wallace, O'Sullivan Orla, Desmond G Higgins
    posted to alignment evolution methods multiple by zmasek on 2006-07-25 19:49:39 as **
  • Automated de novo identification of repeat sequence families in sequenced genomes.
    Genome Res, Vol. 12, No. 8. (August 2002), pp. 1269-1276.
    by Z Bao, SR Eddy
    posted to 213 alignment cited clustering multiplealign recon te by yoanjacquemin on 2008-01-15 15:47:59 as read along with 5 people Neeperando aprasad timflutre Jporci urgi
  • GMAP: a genomic mapping and alignment program for mRNA and EST sequences
    Bioinformatics, Vol. 21, No. 9. (1 May 2005), pp. 1859-1875.
    by Thomas D Wu, Colin K Watanabe
    posted to alignment detection by yoanjacquemin on 2008-01-16 08:29:19 as read along with 1 person olympos
  • The many faces of sequence alignment.
    Brief Bioinform, Vol. 6, No. 1. (March 2005), pp. 6-22.
    by S Batzoglou
    posted to alignment bg by yoanjacquemin on 2008-01-16 08:25:23 as read along with 4 people and 2 groups balajis dpollard sdvillal gjuggler Bioinformatics 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 alignment bg suffixtree te by yoanjacquemin on 2008-01-15 08:23:57 as read along with 2 people and 1 group indigoviolet adijr EisenLab
  • Using BLAST for identifying gene and protein names in journal articles
    Gene, Vol. 259, No. 1-2. (23 December 2000), pp. 245-252.
    by Michael Krauthammer, Andrey Rzhetsky, Pavel Morozov, Carol Friedman
    posted to sequence ner alignment by yggdrasil on 2008-05-15 10:49:16 as ** along with 4 people and 1 group klo yas bhaddow vlachmore T_lab
  • Multiple sequence alignment with the Clustal series of programs.
    Nucleic Acids Res, Vol. 31, No. 13. (1 July 2003), pp. 3497-3500.
    by R Chenna, H Sugawara, T Koike, R Lopez, TJ Gibson, DG Higgins, JD Thompson
    posted to alignment bioinformatics by xingxu on 2008-03-18 19:10:59 as ** along with 4 people and 1 group miguel chad_davis beatrizfernandez raylim Microbial-Ecology
  • CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
    Nucleic Acids Res, Vol. 22, No. 22. (11 November 1994), pp. 4673-4680.
    by JD Thompson, DG Higgins, TJ Gibson
    posted to alignment bioinformatics by xingxu on 2008-03-19 23:47:59 as ** along with 23 people and 1 group Lombardo_7 newton1234 jmw greger_halltorp jshapiro mercaptan evaf caldavis miguel onlyrey bjorns aprasad RMGraze moborg arcticrasta dullhunk caporaso ahanora Haggan BioNica leelarcombe timflutre adijr biomedical-nlp
  • SeqMap : mapping massive amount of oligonucleotides to the genome
    Bioinformatics (12 August 2008), btn429.
    by Hui Jiang, Wing H Wong
    posted to microarray alignment by waszak on 2008-08-15 15:31:51 as ** along with 1 person GeeSharpMinor
  • SOAP: short oligonucleotide alignment program.
    Bioinformatics (28 January 2008)
    by Ruiqiang Li, Yingrui Li, Karsten Kristiansen, Jun Wang
    posted to microarray alignment by waszak on 2008-08-18 14:35:44 as ** along with 8 people bozdagd urgi caseybrown jyuh ghattem GustavoLacerda niallhaslam mdimon
  • An adaptive and iterative algorithm for refining multiple sequence alignment.
    Comput Biol Chem, Vol. 28, No. 2. (April 2004), pp. 141-148.
    by Y Wang, KB Li
    posted to alignment multiple by wallacei on 2004-11-16 14:50:42
  • notes MUSCLE: a multiple sequence alignment method with reduced time and space complexity.
    BMC Bioinformatics, Vol. 5, No. 1. (19 August 2004)
    by RC Edgar
    posted to alignment multiple by wallacei on 2004-11-16 14:49:29 along with 13 people and 3 groups Ema sanchezbuelna knaseanka chrn jwm balajis gbart caporaso sriram_s cdallett timflutre gisle urgi Radiation_Damage Stressosome biomedical-nlp
  • A method for aligning RNA secondary structures and its application to RNA motif detection.
    BMC Bioinformatics, Vol. 6 (2005)
    by J Liu, JT Wang, J Hu, B Tian
    posted to rna alignment by vwchan on 2007-02-01 12:38:57 as ** along with 2 people and 1 group arcticrasta emidio_capriotti beta
  • Family relationships: should consensus reign?--consensus clustering for protein families.
    Bioinformatics, Vol. 23, No. 2. (15 January 2007)
    by M Nikolski, DJ Sherman
    posted to alignment clustering protein by vwchan on 2007-04-01 21:33:54 as ** along with 1 group beta
  • DUSTer: A Method for Unraveling Cross-Language Divergences for Statistical Word-Level Alignment
    (2002)
    by B Dorr, L Pearl, R Hwa, N Habash
    posted to alignment divergence overcome by veer on 2007-03-31 12:48:42 as read
  • The CMU Statistical Machine Translation System
    (2003)
    by S Vogel, Y Zhang, F Huang, A Tribble, A Venugopal, B Zhao, A Waibel
    posted to alignment and integrated isa machine phrase segmentation smt statistical translation by veer on 2007-04-07 11:16:13 as *****
  • Structural Matching of Parallel Texts
    (1993)
    by Y Matsumoto, H Ishimoto, T Utsuro
    posted to alignment disjuctive node or structural by veer on 2007-05-14 14:47:08 as read
  • PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data
    BMC Bioinformatics, Vol. 7 (25 August 2006), 390.
    by Kuo P Chiu, Chee-Hong Wong, Qiongyu Chen, Pramila Ariyaratne, Hong S Ooi, Chia-Lin Wei, Wing-Kin K Sung, Yijun Ruan
    posted to alignment mapping short-reads software by urgi on 2008-04-08 10:58:50 as ** along with 1 person jyuh
  • High-throughput sequence alignment using Graphics Processing Units
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Michael Schatz, Cole Trapnell, Arthur Delcher, Amitabh Varshney
    posted to alignment gpu high_throughput mummer sequence short-reads software technologies by urgi on 2008-04-01 18:20:14 as ** along with 10 people and 1 group Yanno jyuh sephy lusk laughcry nedwards mdimon cndewey heliopais tpreeprem gatech-compgenomics
  • Identification and characterization of multi-species conserved sequences.
    Genome Res, Vol. 13, No. 12. (December 2003), pp. 2507-2518.
    by EH Margulies, M Blanchette, D Haussler, ED Green,
    posted to alignment bioinformatics comparative genomics multiple by ujh on 2005-03-03 10:51:27 as read along with 5 people and 1 group nklee operon brant sujaikumar bezdan 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 alignment bioinformatics multiple by ujh on 2005-03-03 10:50:37 as read along with 8 people and 1 group AlexanderPico yylin Neeperando maralena operon indigoviolet csardas djkt EisenLab
  • Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology
    (15 January 1997)
    by Dan Gusfield
    posted to alignment bioinformatics by ujh on 2005-04-18 15:44:00 as *** along with 11 people and 1 group reyez ep161302 creswick tijl grzegorz luispedro emranmohdtamil hoangmit thonnardo pool007 nedwards Pattern-Analysis
  • Localized alpha4 integrin phosphorylation directs shear stress-induced endothelial cell alignment.
    Circulation research, Vol. 103, No. 2. (18 July 2008), pp. 177-185.
    by LE Goldfinger, E Tzima, R Stockton, WB Kiosses, K Kinbara, E Tkachenko, E Gutierrez, A Groisman, P Nguyen, S Chien, MH Ginsberg
    posted to shear rac integrin endothelial alignment by tsjipko on 2008-07-21 10:35:53 as ***
  • Interstitial fluid flow induces myofibroblast differentiation and collagen alignment in vitro
    J Cell Sci, Vol. 118, No. 20. (15 October 2005), pp. 4731-4739.
    by Chee P Ng, Boris Hinz, Melody A Swartz
    posted to transform method histogram fourier fibers fft alignment by tsjipko on 2008-06-06 14:24:22 as ****
  • Electrical stimulation directly induces pre-angiogenic responses in vascular endothelial cells by signaling through VEGF receptors.
    Journal of cell science, Vol. 117, No. Pt 3. (26 January 2004), pp. 397-405.
    by M Zhao, H Bai, E Wang, JV Forrester, CD McCaig
    posted to vegfr2 vegf rho huvec endothelial electrotaxis electrical angiogenesis alignment by tsjipko on 2008-06-15 18:14:26 as **
  • p38 Mitogen-Activated Protein Kinase Activation in Endothelial Cell Is Implicated in Cell Alignment and Elongation Induced by Fluid Shear Stress
    Endothelium, Vol. 13, No. 1. (February 2006), pp. 43-50.
    by Takayuki Kadohama, Nobuyuki Akasaka, Kengo Nishimura, Yuji Hoshino, Tadahiro Sasajima, Bauer Sumpio
    posted to alignment elongation endothelial p38 shear by tsjipko on 2006-09-18 08:42:21 as **
  • Correspondences between low-energy modes in enzymes: Dynamics-based alignment of enzymatic functional families
    Protein Sci, Vol. 17, No. 5. (1 May 2008), pp. 918-929.
    by Andrea Zen, Vincenzo Carnevale, Arthur M Lesk, Cristian Micheletti
    posted to enzyme_dynamics dynamics alignment by tny on 2008-08-20 03:55:00 as ** along with 2 people and 1 group edvin skoddet Nielsen group
  • Metabolic pathways variability and sequence/networks comparisons.
    BMC Bioinformatics, Vol. 7 (2006)
    by K Tun, PK Dhar, MC Palumbo, A Giuliani
    posted to alignment comparative metabolism network by tny on 2006-05-19 14:31:06 as **
  • Evolution at the nucleotide level: the problem of multiple whole-genome alignment.
    Hum Mol Genet, Vol. 15 Suppl 1 (15 April 2006)
    by CN Dewey, L Pachter
    posted to alignment evolution review by tny on 2006-05-30 06:26:35 as ** along with 6 people and 2 groups Neeperando operon Ayest dchughes AaronDarling echinotrix G4ID Genetics-of-Gambling
  • The accuracy of several multiple sequence alignment programs for proteins
    BMC Bioinformatics, Vol. 7 (24 October 2006), 471.
    by Paulo AS Nuin, Zhuozhi Wang, Elisabeth RM Tillier
    posted to alignment test by tny on 2006-10-25 12:55:09 as ** along with 2 people plofje rabio
  • A systematic comparison of various statistical alignment models
    Comput. Linguist., Vol. 29, No. 1. (March 2003), pp. 19-51.
    by Franz J Och, Hermann Ney
    posted to naturallanguage hmm graphicalmodels graphicalmodel alignment by tkollar on 2008-07-31 16:13:15 as ** along with 1 person bhaddow
  • HMM-based word alignment in statistical translation
    (1996), pp. 836-841.
    by Stephan Vogel, Hermann Ney, Christoph Tillmann
    posted to naturallanguage hmm graphicalmodels graphicalmodel alignment by tkollar on 2008-07-31 16:10:56 as *** along with 4 people and 1 group snifty frcchang vamshi kvorg NLP
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