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Tag msa [118 articles]

Recent papers classified by the tag msa.
  • Recent Evolutions of Multiple Sequence Alignment Algorithms
    PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e123.
    by Cédric Notredame
    posted to algorithm bioinformatics msa by skhadar on 2008-02-27 06:56:54 as ** along with 4 people and 1 group agustinarce sobolevnrm hpaces mingzhi baker-group
  • Multiple system atrophy
    The Lancet Neurology, Vol. 3, No. 2. (February 2004), pp. 93-103.
    by Gregor K Wenning, Carlo Colosimo, Felix Geser, Werner Poewe
    posted to msa by psique on 2008-05-28 17:07:03 as read along with 1 group parkinson's disease references
  • The role of α-synuclein in the pathogenesis of multiple system atrophy
    Acta Neuropathologica, Vol. 109, No. 2. (5 February 2005), pp. 129-140.
    by Gregor K Wenning, Kurt A Jellinger
    posted to msa synuclein by psique on 2008-05-28 17:07:56 as read along with 1 group parkinson's disease references
  • Neuropathological spectrum of synucleinopathies.
    Movement disorders : official journal of the Movement Disorder Society, Vol. 18 Suppl 6 (September 2003)
    by KA Jellinger
    posted to pd msa synuclein by psique on 2008-05-28 17:08:43 as read along with 1 group parkinson's disease references
  • Cellular pathology of multiple system atrophy: a review.
    Journal of neurology, neurosurgery, and psychiatry, Vol. 57, No. 2. (February 1994), pp. 129-133.
    by PL Lantos, MI Papp
    posted to msa synuclein by psique on 2008-05-28 16:58:51 as read along with 1 group parkinson's disease references
  • Confidence in comparative genomics
    Genome Res., Vol. 18, No. 2. (1 February 2008), pp. 199-200.
    by Elliott H Margulies
    posted to review msa comparative_genomics commentary by pengchy on 2008-10-04 02:44:20 as ** along with 5 people treangen djkt xingxu maximilianh boudinot
  • Print Is Flat, Code Is Deep: The Importance of Media-Specific Analysis
    Poetics Today, Vol. 25, No. 1. (13 April 2004), pp. 67-90.
    by Katherine N Hayles
    posted to code hypertext msa text by paulswartz on 2006-10-16 12:27:29 as read
  • Differentiating multiple system atrophy from Parkinson's disease: contribution of striatal and midbrain MRI volumetry and multi-tracer PET imaging.
    J Neurol Neurosurg Psychiatry, Vol. 73, No. 5. (November 2002), pp. 517-523.
    by M Ghaemi, R Hilker, J Rudolf, J Sobesky, WD Heiss
    posted to dopamine fdg f-dopa mri msa pd pet raclopride by ntvandehey on 2007-08-02 22:30:27 as ***
  • Three-dimensional profiles: a new tool to identify protein surface similarities.
    J Mol Biol, Vol. 284, No. 4. (11 December 1998), pp. 1211-1221.
    by M de Rinaldis, G Ausiello, G Cesareni, M Helmer-Citterich
    posted to algorithm application msa pattern pdb structure-searching surface by nickolay on 2005-12-08 23:39:24 as ** along with 1 person dgront
  • Protein structure: geometry, topology and classification
    Reports of Progress in Physics, Vol. 64 (April 2001), pp. 517-590.
    by WR Taylor, ACW May, NP Brown, A Aszódi
    posted to domain-classification geometric-hashing graph-theory machine-learning msa pattern review structure-classification surface topology by nickolay on 2005-12-08 23:43:43 as ****
  • An information theoretic approach to macromolecular modeling: I. Sequence alignments.
    Biophys J, Vol. 89, No. 5. (November 2005), pp. 2998-3007.
    by T Aynechi, ID Kuntz
    posted to algorithm information-theory msa by nickolay on 2005-12-06 01:46:03 as **** along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
  • MUSTA--a general, efficient, automated method for multiple structure alignment and detection of common motifs: application to proteins.
    J Comput Biol, Vol. 8, No. 2. (2001), pp. 93-121.
    by N Leibowitz, R Nussinov, HJ Wolfson
    posted to algorithm geometric-hashing msa by nickolay on 2005-12-06 01:58:26 as **
  • 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 msa by newton1234 on 2008-06-17 21:12:55 as ** along with 24 people and 1 group usagi-kirin jmw greger_halltorp jshapiro mercaptan evaf caldavis miguel onlyrey bjorns aprasad RMGraze moborg arcticrasta dullhunk caporaso ahanora Haggan BioNica leelarcombe timflutre adijr xingxu Lombardo_7 biomedical-nlp
  • Gap costs for multiple sequence alignment.
    Journal of theoretical biology, Vol. 138, No. 3. (8 June 1989), pp. 297-309.
    by SF Altschul
    posted to alignment msa by newton1234 on 2008-06-17 21:00:38 as **
  • Multiple sequence alignment by parallel simulated annealing.
    CABIOS, Vol. 9, No. 3. (June 1993), pp. 267-273.
    by M Ishikawa, T Toya, M Hoshida, K Nitta, A Ogiwara, M Kanehisa
    posted to alignment msa by newton1234 on 2008-06-17 21:18:18 as **
  • BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs
    Bioinformatics, Vol. 15, No. 1. (1 January 1999), pp. 87-88.
    by Jd Thompson, F Plewniak, O Poch
    posted to alignment msa by newton1234 on 2008-06-17 23:10:26 as ** along with 1 person BioNica
  • Weights for data related by a tree.
    J. Mol. Biol., Vol. 207, No. 4. (20 June 1989), pp. 647-653.
    by SF Altschul, RJ Carroll, DJ Lipman
    posted to alignment msa by newton1234 on 2008-06-17 21:01:51 as ** along with 1 person nuke2005
  • SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures.
    Bioinformatics, Vol. 21, No. 18. (15 September 2005), pp. 3615-3621.
    by H Zhou, Y Zhou
    posted to alignment msa by newton1234 on 2008-06-17 21:16:06 as **
  • Multiple sequence alignment using simulated annealing
    CABIOS, Vol. 10, No. 4. (1 July 1994), pp. 419-426.
    by Jin Kim, Sakti Pramanik, Moon J Chung
    posted to alignment msa by newton1234 on 2008-06-17 21:20:47 as **
  • PROMALS: towards accurate multiple sequence alignments of distantly related proteins
    Bioinformatics, Vol. 23, No. 7. (1 April 2007), pp. 802-808.
    by Pei, Jimin, Grishin, V Nick
    posted to alignment msa by newton1234 on 2008-06-17 23:16:16 as **
  • Multiple DNA and protein sequence alignment based on segment-to-segment comparison
    Proceedings of the National Academy of Sciences, Vol. 93, No. 22. (29 October 1996), pp. 12098-12103.
    by Burkhard Morgenstern, Andreas Dress, Thomas Werner
    posted to alignment msa by newton1234 on 2008-06-25 17:11:36 as ** along with 2 people adijr gjuggler
  • Recent progress in multiple sequence alignment: a survey.
    Pharmacogenomics, Vol. 3, No. 1. (January 2002), pp. 131-144.
    by C Notredame
    posted to alignment msa by newton1234 on 2008-06-17 20:58:54 as **
  • Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments.
    Proteins, Vol. 58, No. 2. (1 February 2005), pp. 321-328.
    by H Zhou, Y Zhou
    posted to alignment msa by newton1234 on 2008-06-17 21:17:33 as ** along with 1 person j3xucite
  • A novel randomized iterative strategy for aligning multiple protein sequences.
    Computer applications in the biosciences : CABIOS, Vol. 7, No. 4. (October 1991), pp. 479-484.
    by MP Berger, PJ Munson
    posted to alignment msa by newton1234 on 2008-06-17 21:25:22 as **
  • MUSCLE: multiple sequence alignment with high accuracy and high throughput.
    Nucleic Acids Res., Vol. 32, No. 5. (2004), pp. 1792-1797.
    by RC Edgar
    posted to alignment msa by newton1234 on 2008-06-17 21:13:52 as ** along with 18 people and 2 groups sebk agustinarce fhsantanna nachtalp bpb chrn jwm Haggan sanchezbuelna timflutre olympos martainn edvin skumagai bmaust sconlan dmp kcrawlik Radiation_Damage Stressosome
  • 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 alignment msa by newton1234 on 2008-06-17 21:14:35 as ** along with 9 people and 1 group miguel dayjm indigoviolet ffranca treangen Haggan siebertm adijr marti EisenLab
  • HOMSTRAD: a database of protein structure alignments for homologous families.
    Protein Sci., Vol. 7, No. 11. (November 1998), pp. 2469-2471.
    by K Mizuguchi, CM Deane, TL Blundell, JP Overington
    posted to alignment msa by newton1234 on 2008-06-17 23:13:01 as ** along with 6 people bicko chrn massivemayhem medic0747 cdeane sebk
  • On the complexity of multiple sequence alignment.
    J. Comput. Biol., Vol. 1, No. 4. (1994), pp. 337-348.
    by L Wang, T Jiang
    posted to alignment msa by newton1234 on 2008-06-17 21:03:46 as ** along with 2 people treangen yylin
  • ProbCons: Probabilistic consistency-based multiple sequence alignment.
    Genome Res., Vol. 15, No. 2. (February 2005), pp. 330-340.
    by CB Do, MS Mahabhashyam, M Brudno, S Batzoglou
    posted to alignment msa by newton1234 on 2008-06-17 21:24:26 as ** along with 6 people and 1 group bpb radek balajis stajich olympos gjuggler Berkeley Mycology
  • SAGA: sequence alignment by genetic algorithm.
    Nucleic Acids Res., Vol. 24, No. 8. (15 April 1996), pp. 1515-1524.
    by C Notredame, DG Higgins
    posted to alignment msa by newton1234 on 2008-06-17 21:23:30 as **
  • Simulated annealing algorithm for the multiple sequence alignment problem: the approach of polymers in a random medium.
    Phys. Rev. E, Vol. 72, No. 3 Pt 1. (September 2005), 031915.
    by M Hernández-Guía, R Mulet, S Rodríguez-Pérez
    posted to alignment msa by newton1234 on 2008-06-17 21:22:43 as **
  • PROMALS3D: a tool for multiple protein sequence and structure alignments.
    Nucleic Acids Res (20 February 2008)
    by Jimin Pei, Bong-Hyun H Kim, Nick V V Grishin
    posted to alignment msa by newton1234 on 2008-03-12 07:20:01 as ** along with 2 people and 1 group sunhwan sobolevnrm baker-group
  • PROMALS web server for accurate multiple protein sequence alignments.
    Nucleic Acids Res, Vol. 35, No. Web Server issue. (July 2007)
    by J Pei, BH Kim, M Tang, NV Grishin
    posted to alignment msa by newton1234 on 2008-03-12 07:21:42 as **
  • Progressive sequence alignment as a prerequisite to correct phylogenetic trees.
    J. Mol. Evol., Vol. 25, No. 4. (1987), pp. 351-360.
    by DF Feng, RF Doolittle
    posted to alignment msa by newton1234 on 2008-06-17 21:12:10 as ** along with 3 people balajis nuke2005 AaronDarling
  • PROMALS: towards accurate multiple sequence alignments of distantly related proteins.
    Bioinformatics, Vol. 23, No. 7. (1 April 2007), pp. 802-808.
    by J Pei, NV Grishin
    posted to alignment msa by newton1234 on 2008-03-12 07:20:47 as **
  • COFFEE: an objective function for multiple sequence alignments.
    Bioinformatics, Vol. 14, No. 5. (June 1998), pp. 407-422.
    by C Notredame, L Holm, DG Higgins
    posted to alignment msa by newton1234 on 2008-06-17 21:02:50 as **
  • Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee.
    Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006)
    by F Armougom, S Moretti, O Poirot, S Audic, P Dumas, B Schaeli, V Keduas, C Notredame
    posted to msa by marti on 2008-01-23 16:14:59 as read
  • An evaluation of automated homology modelling methods at low target template sequence similarity
    Bioinformatics, Vol. 23, No. 15. (1 August 2007), pp. 1901-1908.
    by James A Dalton, Richard M Jackson
    posted to homology-modelling msa by marti on 2008-08-07 15:13:47 as *** along with 5 people cdeane chad_davis biehl neils pansapiens
  • Recent Evolutions of Multiple Sequence Alignment Algorithms
    PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e123.
    by Cédric Notredame
    posted to msa review by marti on 2008-01-23 16:13:51 as read along with 10 people and 2 groups mdimmic rvosa timflutre stajich zwang cabbagezs groepl yoanjacquemin smbe2008 giovenko Bioinformatics FAB-lab
  • MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
    Nucleic Acids Res, Vol. 30, No. 14. (15 July 2002), pp. 3059-3066.
    by K Katoh, K Misawa, K Kuma, T Miyata
    posted to msa by marti on 2008-01-24 15:32:45 as * along with 5 people treangen zmasek rabio timflutre urgi
  • Analysis and prediction of functional sub-types from protein sequence alignments
    Journal of Molecular Biology, Vol. 303, No. 1. (13 October 2000), pp. 61-76.
    by Sridhar S Hannenhalli, Robert B Russell
    posted to alignments hmm msa prediction by marti on 2008-05-07 18:00:32 as *** along with 1 person and 2 groups barry structural_bioinformatics Bioinformatics
  • The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.
    Nucleic Acids Res (25 May 2007)
    by Sebastien Moretti, Fabrice Armougom, Iain M M Wallace, Desmond G G Higgins, Cornelius V V Jongeneel, Cedric Notredame
    posted to msa by marti on 2008-01-23 16:14:47 as read along with 2 people and 2 groups marcius sebastien_vigneau BioinfoCIPF SGU-CIPF
  • 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 msa phylogeny by marti on 2008-08-07 15:16:49 as read along with 22 people and 3 groups bpcusack chad_davis hpaces dinnes gjuggler djkt ArtemPankin phoenixzxl jago marck imtechnology aprasad zwang bmaust bpb michaelbarton Schmidtc AbnerCYH gulsacan emptyhb jlgreen nuin Khavkin's lab iSEEM Green Lab
  • Multiple protein sequence alignment
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Jimin Pei
    posted to msa by marck on 2008-06-22 08:55:46 as ** along with 5 people and 1 group agustinarce zwang TOchi paulschlesinger sobolevnrm baker-group
  • R-Coffee: a method for multiple alignment of non-coding RNA.
    Nucleic acids research (17 April 2008)
    by Andreas Wilm, Desmond G G Higgins, Cédric Notredame
    posted to msa rna by marck on 2008-05-30 05:11:54 as ** along with 2 people urgi Neeperando
  • Clustal W and Clustal X version 2.0
    Bioinformatics, Vol. 23, No. 21. (1 November 2007), pp. 2947-2948.
    by MA Larkin, G Blackshields, NP Brown, R Chenna, PA Mcgettigan, H Mcwilliam, F Valentin, IM Wallace, A Wilm, R Lopez, JD Thompson, TJ Gibson, DG Higgins
    posted to clustalw msa by marck on 2008-08-30 09:37:14 as ** along with 6 people cassj lisa1 ryanraaum bmaust alanrw mschofie
  • 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 clustalw msa by marck on 2008-08-30 09:37:29 as ** along with 5 people and 1 group miguel chad_davis beatrizfernandez raylim xingxu Microbial-Ecology
  • Protein multiple sequence alignment.
    Methods in molecular biology (Clifton, N.J.), Vol. 484 (2008), pp. 379-413.
    by CB Do, K Katoh
    posted to msa by marck on 2008-07-03 10:58:56 as **
  • Allosteric determinants in guanine nucleotide-binding proteins.
    Proc Natl Acad Sci U S A, Vol. 100, No. 24. (25 November 2003), pp. 14445-14450.
    by ME Hatley, SW Lockless, SK Gibson, AG Gilman, R Ranganathan
    posted to msa by lna on 2005-10-06 11:25:30 as ***** along with 4 people and 5 groups barry Einat marcius caporaso structural_bioinformatics Bioinformatics biomedical-nlp BioinfoCIPF SGU-CIPF
  • Evolutionary information for specifying a protein fold
    Nature, Vol. 437, No. 7058., pp. 512-518.
    by Michael Socolich, Steve W Lockless, William P Russ, Heather Lee, Kevin H Gardner, Rama Ranganathan
    posted to msa by lna on 2006-09-04 14:06:14 as * along with 14 people and 5 groups ana barry bpb Einat balajis marcius gbart analogAI nirfriedman caporaso massivemayhem mingzhi bethbromley ca3295 structural_bioinformatics Bioinformatics biomedical-nlp BioinfoCIPF SGU-CIPF
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