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Tag sequence_alignment [98 articles]

Recent papers classified by the tag sequence_alignment.
  • Sequence alignment approach to pick up conformationally similar protein fragments.
    J Mol Biol, Vol. 223, No. 4. (20 February 1992), pp. 1053-1061.
    by AS Kolaskar, U Kulkarni-Kale
    posted to sequence_alignment substitution_matrix by vavi on 2006-07-16 16:35:06 as **
  • Identification of common molecular subsequences.
    J Mol Biol, Vol. 147, No. 1. (25 March 1981), pp. 195-197.
    by TF Smith, MS Waterman
    posted to sequence_alignment by vavi on 2006-07-16 11:17:34 as * along with 8 people newton1234 creswick bicko dgront rabio cjeans incovoma sujaikumar
  • An improved algorithm for matching biological sequences.
    J Mol Biol, Vol. 162, No. 3. (15 December 1982), pp. 705-708.
    by O Gotoh
    posted to sequence_alignment by vavi on 2006-07-16 11:01:49 as ** along with 2 people adijr jofiel
  • Determination of reliable regions in protein sequence alignments
    Protein Engineering, Vol. 3, No. 7. (July 1990), pp. 565-569.
    by M Vingron, P Argos
    posted to alignment_quality sequence_alignment by rabio on 2006-12-05 12:59:37 as **
  • Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 87, No. 6. (March 1990), pp. 2264-2268.
    by Samuel Karlin, Stephen F Altschul
    posted to sequence_alignment sequene_features statistics by rabio on 2007-02-16 17:04:06 as read along with 7 people and 1 group kaspermunch AaronDarling timflutre cjeans siebertm adijr karfunkel Bioinformatics
  • Comparative modeling without implicit sequence alignments
    Bioinformatics, Vol. 23, No. 19. (27 July 2007), pp. 2522-2527.
    by Andrzej Kolinski, Dominik Gront
    posted to comparative_modeling sequence_alignment by rabio on 2007-10-25 13:57:57 as read along with 2 people carlescorbi sekmi
  • Contact-based sequence alignment
    Nucleic Acids Research, Vol. 32, No. 8. (30 April 2004), pp. 2464-2473.
    by Jens Kleinjung, John Romein, Kuang Lin, Jaap Heringa
    posted to sequence_alignment by rabio on 2007-07-19 13:03:17 as ** along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
  • Stochastic pairwise alignments
    Bioinformatics, Vol. 18, No. Suppl 2. (2002), pp. S152-S160.
    by U Mückstein, IL Hofacker, PF Stadler
    posted to probabilistic_alignment sequence_alignment suboptimal_alignment by rabio on 2006-12-10 21:56:59 as read along with 1 person dgront
  • Generalized affine gap costs for protein sequence alignment
    Proteins, Vol. 32, No. 1. (1 July 1998), pp. 88-96.
    by Stephen F Altschul
    posted to gap_cost sequence_alignment by rabio on 2007-02-19 14:42:00 as read
  • Automata-theoretic models of mutation and alignment.
    Proceedings of the International Conference on Intelligent Systems for Molecular Biology, Vol. 3 (1995), pp. 341-349.
    by DB Searls, KP Murphy
    posted to sequence_alignment by rabio on 2007-05-16 15:42:40 as **
  • Dynamite: a flexible code generating language for dynamic programming methods used in sequence comparison.
    Proceedings of the International Conference on Intelligent Systems for Molecular Biology, Vol. 5 (1997), pp. 56-64.
    by E Birney, R Durbin
    posted to dynamic_programming sequence_alignment by rabio on 2007-05-16 15:40:44 as ** along with 1 person wenhan
  • Biological Sequence Analysis : Probabilistic Models of Proteins and Nucleic Acids
    (01 July 1999)
    by Richard Durbin, Sean R Eddy, Anders Krogh, Graeme Mitchison
    posted to hmm profile sequence_alignment sequence_analysis sequence_profile sequence_similarity substitution_matrices by rabio on 2007-02-23 14:51:30 as *** along with 10 people and 1 group derek_farn stanley ujh pcahan1 balajis indigoviolet moborg emranmohdtamil dullhunk wenhan EisenLab
  • Quantification of the variation in percentage identity for protein sequence alignments
    BMC Bioinformatics, Vol. 7 (19 September 2006), 415.
    by Ps G Raghava, Geoffrey J Barton
    posted to sequence_alignment by rabio on 2007-03-02 16:29:23 as read along with 5 people and 1 group pansapiens bicko dpollard medic0747 sujaikumar EisenLab
  • Alignment Metric Accuracy
    (27 Oct 2005)
    by Ariel S Schwartz, Eugene W Myers, Lior Pachter
    posted to alignment_quality measure metric multiple_sequence_alignment sequence_alignment by rabio on 2007-01-12 14:25:42 as ***
  • Clustering protein sequences--structure prediction by transitive homology
    Bioinformatics, Vol. 17, No. 10. (1 October 2001), pp. 935-941.
    by Eva Bolten, Alexander Schliep, Sebastian Schneckener, Dietmar Schomburg, Rainer Schrader
    posted to sequence_alignment clustering by rabio on 2007-01-30 16:42:12 as ** along with 1 person dgront
  • A unified statistical framework for sequence comparison and structure comparison
    PNAS, Vol. 95, No. 11. (26 May 1998), pp. 5913-5920.
    by Michael Levitt, Mark Gerstein
    posted to sequence_alignment structure_alignment by rabio on 2007-03-02 16:25:00 as ** along with 1 person dgront
  • MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
    Nucleic Acids Research, Vol. 30, No. 14. (15 July 2002), pp. 3059-3066.
    by K Katoh, K Misawa, K Kuma, T Miyata
    posted to sequence_alignment multiple_sequence_alignment tools by rabio on 2007-01-26 17:39:11 as read along with 5 people urgi treangen zmasek timflutre marti
  • Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families
    Science, Vol. 286, No. 5438. (08 October 1999), pp. 295-299.
    by Steve W Lockless, Rama Ranganathan
    posted to suboptimal_alignment sequence_alignment by rabio on 2007-01-30 16:37:43 as ** along with 15 people and 5 groups stevanspringer Einat marcius eckart_bindewald analogAI dgront caporaso sriram_s choonpeng Haggan mottonen zambujo mingzhi bethbromley ca3295 structural_bioinformatics FAB-lab biomedical-nlp BioinfoCIPF SGU-CIPF
  • Where did the BLOSUM62 alignment score matrix come from?
    Nature Biotechnology, Vol. 22, No. 8. (August 2004), pp. 1035-1036.
    by Sean R Eddy
    posted to sequence_alignment sequence_similarity by rabio on 2007-02-15 02:31:15 as read along with 5 people reyez ziquje bicko gurkanbebek xiaobeizhao
  • Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection
    Nucleic Acids Research, Vol. 34, No. 17. (September 2006), e112.
    by Dylan Chivian, David Baker
    posted to homology_modeling parametric_alignment sequence_alignment suboptimal_alignment by rabio on 2007-03-02 16:15:05 as read along with 2 people jwm dgront
  • Accuracy of structure-based sequence alignments of automatic methods
    BMC Bioinformatics, Vol. 8 (20 September 2007), 355.
    by Changhoon Kim, Byungkook Lee
    posted to sequence_alignment structure_alignment by rabio on 2007-12-31 02:58:24 as read along with 3 people dimka chad_davis zwang
  • MAFFT version 5: improvement in accuracy of multiple sequence alignment.
    Nucleic Acids Research, Vol. 33, No. 2. (2005), pp. 511-518.
    by K Katoh, K Kuma, H Toh, T Miyata
    posted to sequence_alignment multiple_sequence_alignment tools by rabio on 2007-01-25 15:14:22 as read along with 3 people and 1 group urgi caporaso timflutre biomedical-nlp
  • Rapid significance estimation in local sequence alignment with gaps
    Journal of Computational Biology, Vol. 9, No. 2. (April 2002), pp. 243-260.
    by Ralf Bundschuh
    posted to alignment_quality sequence_alignment by rabio on 2007-05-25 14:20:14 as **
  • Probabilistic Sequence Alignments: Realistic Models with Efficient Algorithms
    Physical Review Letters, Vol. 98, No. 7. (12 February 2007)
    by Edouard Yeramian, Edouard Debonneuil
    posted to probabilistic_alignment sequence_alignment by rabio on 2007-02-14 23:15:31 as read
  • A novel approach to local reliability of sequence alignments
    Bioinformatics, Vol. 18, No. 6. (1 June 2002), pp. 847-854.
    by Maximilian Schlosshauer, Mattias Ohlsson
    posted to probabilistic_alignment sequence_alignment suboptimal_alignment by rabio on 2006-11-30 14:30:37 as read
  • Statistical Significance of Probabilistic Sequence Alignment and Related Local Hidden Markov Models
    Journal of Computational Biology, Vol. 8, No. 3. (2001), pp. 249-282.
    by Yi K Yu, Terence Hwa
    posted to alignment_quality hmm probabilistic_alignment sequence_alignment sequence_analysis by rabio on 2007-02-14 22:51:45 as ***
  • A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons
    Journal of Molecular Biology, Vol. 197, No. 4. (20 October 1987), pp. 723-728.
    by Michael S Waterman, Mark Eggert
    posted to suboptimal_alignment sequence_alignment by rabio on 2007-02-01 17:29:37 as read
  • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    Nucleic Acids Research, 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 sequence_alignment by rabio on 2006-12-05 14:03:55 as ** along with 42 people and 4 groups granujilla newton1234 david_parsons edvin bandrewfox mariakmejia knaseanka setar iakes miguel kaarsinogen bjorns bicko jmeppley chad_davis balajis nuke2005 eweaver indigoviolet dullhunk robert dgront happy_manatee caporaso treangen kengg manzanita leelarcombe CitoJam jdelcampo aengisch massivemayhem mirzazadeh azazello sujaikumar beatrizfernandez GustavoLacerda siebertm adijr viktor21614 mijam grottenolm EisenLab biomedical-nlp Microbial-Ecology Plantandetc
  • Basic local alignment search tool
    Journal of Molecular Biology, Vol. 215, No. 3. (5 October 1990), pp. 403-410.
    by SF Altschul, W Gish, W Miller, EW Myers, DJ Lipman
    posted to sequence_alignment by rabio on 2006-12-05 14:01:52 as *** along with 41 people and 5 groups granujilla benwei ashaytan camster davidng evaf dragonrez jwm jmeppley Ayest RMGraze ea yas balajis alexg indigoviolet moborg arcticrasta dullhunk dgront caporaso michC myui BioNica CitoJam timflutre lusk cjeans incovoma beatrizfernandez wenhan jtomasch GustavoLacerda sgoetz siebertm ichbins81 jofiel Thaverkamp shung marti hervelequere dbk-lab EisenLab T_lab biomedical-nlp Microbial-Ecology
  • Generalized affine gap costs for protein sequence alignment
    Proteins: Structure, Function, and Genetics, Vol. 32, No. 1. (1998), pp. 88-96.
    by Stephen F Altschul
    posted to gap_cost sequence_alignment by rabio on 2006-12-05 13:56:39 as **
  • Predicting reliable regions in protein sequence alignments
    Bioinformatics, Vol. 18, No. 2. (1 February 2002), pp. 306-314.
    by Melissa Cline, Richard Hughey, Kevin Karplus
    posted to alignment_quality sequence_alignment by rabio on 2006-12-05 13:50:22 as ***
  • Dynamic programming algorithms for biological sequence comparison.
    Methods in Enzymology, Vol. 210 (1992), pp. 575-601.
    by WR Pearson, W Miller
    posted to sequence_alignment by rabio on 2007-02-01 17:19:17 as **
  • Near-optimal sequence alignment
    Current Opinion in Structural Biology, Vol. 6, No. 3. (June 1996), pp. 346-352.
    by Martin Vingron
    posted to alignment_quality sequence_alignment suboptimal_alignment by rabio on 2006-12-05 13:36:20 as read
  • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    Journal of Molecular Biology, Vol. 48, No. 3. (March 1970), pp. 443-453.
    by SB Needleman, CD Wunsch
    posted to sequence_alignment by rabio on 2006-12-04 11:59:11 as *** along with 5 people newton1234 yylin jwm dgront incovoma
  • Finite-temperature sequence alignment
    Pacific Symposium on Biocomputing (2000), pp. 624-635.
    by M Kschischo, M Lässig
    posted to probabilistic_alignment sequence_alignment suboptimal_alignment by rabio on 2006-11-30 13:32:48 as read along with 1 person dgront
  • A reliable sequence alignment method based on probabilities of residue correspondences
    Protein Engineering, Vol. 8, No. 10. (1 October 1995), pp. 999-1009.
    by Sanzo Miyazawa
    posted to probabilistic_alignment sequence_alignment suboptimal_alignment by rabio on 2006-11-30 13:31:37 as read along with 1 person dgront
  • 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 bayesian sequence_alignment prediction_ppi by phoenixzxl on 2008-03-14 08:02:52 as ** along with 10 people pansapiens kengg grahamc laughcry zwang biomcgary cabbagezs roys cdeane gjuggler
  • Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes
    Nat Rev Genet, Vol. 9, No. 4. (April 2008), pp. 303-313.
    by Elliott H Margulies, Ewan Birney
    posted to prediction_function review sequence_alignment by phoenixzxl on 2008-03-19 01:26:11 as ** along with 5 people natstreet jyuh zwang mingzhi ptrobajo
  • 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 sequence_alignment evolution by phoenixzxl on 2008-06-20 04:08:46 as **** along with 18 people and 1 group AbnerCYH michaelbarton bpcusack bmaust gulsacan Schmidtc bpb zwang aprasad imtechnology marck ArtemPankin djkt gjuggler hpaces dinnes chad_davis jago Khavkin's lab
  • Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection
    Nucleic Acids Research, Vol. 34, No. 17. (October 2006), pp. e112-e112.
    by D Chivian, D Baker
    posted to algorithms bioinformatics comparative_modeling sequence_alignment by marcius on 2006-10-25 21:43:08 as ** along with 1 person and 2 groups j3xucite BioinfoCIPF SGU-CIPF
  • MicroRNA identification based on sequence and structure alignment.
    Bioinformatics, Vol. 21, No. 18. (15 September 2005), pp. 3610-3614.
    by X Wang, J Zhang, F Li, J Gu, T He, X Zhang, Y Li
    posted to algorithms bioinformatics rna sequence_alignment structure_alignment by marcius on 2005-10-23 03:17:36 as *** along with 2 people and 2 groups eckart_bindewald bioinfo BioinfoCIPF SGU-CIPF
  • Automatic assessment of alignment quality
    Nucleic Acids Research, Vol. 33, No. 22. (2005), pp. 7120-7128.
    by Timo Lassmann, Erik L Sonnhammer
    posted to bioinformatics model_assessment sequence_alignment by marcius on 2006-01-12 19:11:40 as ** along with 1 person and 2 groups BioNica BioinfoCIPF SGU-CIPF
  • Sequence comparison by sequence harmony identifies subtype-specific functional sites
    Nucleic Acids Research, Vol. 34, No. 22. (December 2006), pp. 6540-6548.
    by W Pirovano, KA Feenstra, J Heringa
    posted to bioinformatics classification function protein sequence_alignment by marcius on 2007-01-03 13:02:03 as ** along with 2 people and 2 groups sriram_s marti BioinfoCIPF SGU-CIPF
  • MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons.
    Bioinformatics, Vol. 21, No. 16. (15 August 2005), pp. 3352-3359.
    by S Siebert, R Backofen
    posted to algorithms bioinformatics rna sequence_alignment by marcius on 2005-10-23 03:10:32 as **** along with 2 people and 2 groups arcticrasta ilh BioinfoCIPF SGU-CIPF
  • A benchmark of multiple sequence alignment programs upon structural RNAs.
    Nucleic Acids Res, Vol. 33, No. 8. (2005), pp. 2433-2439.
    by PP Gardner, A Wilm, S Washietl
    posted to bioinformatics rna sequence_alignment by marcius on 2005-10-23 03:09:57 as *** along with 2 groups BioinfoCIPF SGU-CIPF
  • RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space.
    Nucleic Acids Res, Vol. 31, No. 16. (15 August 2003), pp. 4755-4761.
    by CM Duarte, LM Wadley, AM Pyle
    posted to rna secondary_structure sequence_alignment by marcius on 2005-12-28 11:43:12 as ** along with 3 people and 3 groups j3xucite condon emidio_capriotti beta BioinfoCIPF SGU-CIPF
  • Evolutionary plasticity of protein families: Coupling between sequence and structure variation
    Proteins: Structure, Function, and Bioinformatics, Vol. 61, No. 3. (23 September 2005), pp. 535-544.
    by Anna R Panchenko, Yuri I Wolf, Larisa A Panchenko, Thomas Madej
    posted to bioinformatics biophysics evolution sequence_alignment by marcius on 2005-10-23 02:58:31 as ** along with 4 people and 3 groups alexg gbart sobolevnrm insectopalo BioinfoCIPF SGU-CIPF baker-group
  • Grouping of amino acid types and extraction of amino acid properties from multiple sequence alignments using variance maximization
    Proteins: Structure, Function, and Bioinformatics, Vol. 61, No. 3. (23 September 2005), pp. 523-534.
    by James O Wrabl, Nick V Grishin
    posted to aminoacid_alphabets bioinformatics sequence_alignment by marcius on 2005-10-23 02:54:50 as ** along with 2 people and 2 groups Haggan mloewer BioinfoCIPF SGU-CIPF
  • Protein structure prediction in CASP6 using CHIMERA and FAMS.
    Proteins (26 September 2005)
    by Mayuko Takeda-Shitaka, Genki Terashi, Daisuke Takaya, Kazuhiko Kanou, Mitsuo Iwadate, Hideaki Umeyama
    posted to bioinformatics cafasp casp sequence_alignment structure_prediction by marcius on 2005-10-22 09:11:43 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • SAM-T04: what's new in protein-structure prediction for CASP6.
    Proteins (26 September 2005)
    by Kevin Karplus, Sol Katzman, George Shackleford, Martina Koeva, Jenny Draper, Bret Barnes, Marcia Soriano, Richard Hughey
    posted to cafasp casp sequence_alignment structure_prediction by marcius on 2005-10-22 09:10:38 as ** along with 2 groups BioinfoCIPF SGU-CIPF
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