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nedwards's gapped-seeds [33 articles]

当前文献位于 nedwards's 文献库 标签分类为 gapped-seeds. You can also see everyone's gapped-seeds.
  • Multiple spaced seeds for homology search.
    Bioinformatics (5 September 2007)
    by Lucian Ilie, Silvana Ilie
    posted to gapped-seeds seed-strategies sequence-alignment by nedwards on 2008-04-08 15:04:17 as ** along with 2 people treangen cjeans
  • YASS: enhancing the sensitivity of DNA similarity search.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005)
    by L Noé, G Kucherov
    posted to gapped-seeds locality-sensitive-hashing string-indexing string-matching by nedwards on 2007-09-05 16:11:36 as **
  • Generalized correlation functions and their applications in selection of optimal multiple spaced seeds for homology search.
    J Comput Biol, Vol. 14, No. 2. (March 2007), pp. 238-254.
    by Y Kong
    posted to gapped-seeds locality-sensitive-hashing sequence-alignment string-indexing string-matching by nedwards on 2007-09-05 16:09:43 as **
  • On spaced seeds for similarity search
    Discrete Applied Mathematics, Vol. 138, No. 3. (15 April 2004), pp. 253-263.
    by Uri Keich, Ming Li, Bin Ma, John Tromp
    posted to gapped-seeds seed-strategies sequence-alignment string-indexing by nedwards on 2007-09-05 14:00:50 as **
  • PatternHunter: faster and more sensitive homology search.
    Bioinformatics, Vol. 18, No. 3. (March 2002), pp. 440-445.
    by B Ma, J Tromp, M Li
    posted to gapped-seeds inexact-string-matching locality-sensitive-hashing sequence-alignment string-indexing string-matching by nedwards on 2007-08-20 15:01:41 as ** along with 6 people bozdagd nuke2005 catmat treangen natstreet DickSilver
  • 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 alignment-anchors gapped-seeds seed-strategies sequence-alignment by nedwards on 2007-08-17 17:18:20 as ** along with 3 people and 1 group operon indigoviolet treangen EisenLab
  • Efficient Methods for Generating Optimal Single and Multiple Spaced Seeds
    (2004)
    posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 17:26:29 as **
  • Optimizing Multiple Seeds for Protein Homology Search
    IEEE/ACM Trans. Comput. Biol. Bioinformatics, Vol. 2, No. 1. (January 2005), pp. 29-38.
    by Daniel G Brown
    posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 17:26:06 as **
  • Designing multiple simultaneous seeds for DNA similarity search
    (2004), pp. 76-84.
    by Yanni Sun, Jeremy Buhler
    posted to gapped-seeds sequence-alignment string-indexing string-matching by nedwards on 2007-08-14 17:25:12 as **
  • Hardness of Optimal Spaced Seed Design
    Combinatorial Pattern Matching (2005), pp. 144-155.
    by François Nicolas, Eric Rivals
    posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 17:21:29 as **
  • On the complexity of the spaced seeds
    J. Comput. Syst. Sci., Vol. 73, No. 7. (November 2007), pp. 1024-1034.
    by Bin Ma, Ming Li
    posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 17:20:54 as **
  • Multiseed Lossless Filtration
    IEEE/ACM Trans. Comput. Biol. Bioinformatics, Vol. 2, No. 1. (January 2005), pp. 51-61.
    by Gregory Kucherov, Laurent Noe, Mikhail Roytberg
    posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 17:18:58 as ** along with 1 person AaronDarling
  • tPatternHunter: gapped, fast and sensitive translated homology search
    Bioinformatics, Vol. 21, No. 4. (15 February 2005), pp. 542-544.
    by Derek Kisman, Ming Li, Bin Ma, Li Wang
    posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 17:18:14 as **
  • FLASH: A Fast Look-Up Algorithm for String Homology
    (1993), pp. 56-64.
    by Andrea Califano, Isidore Rigoutsos
    posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 17:15:44 as **
  • Better filtering with gapped q-grams
    Fundam. Inf., Vol. 56, No. 1,2. (2003), pp. 51-70.
    by Stefan Burkhardt, Juha Kärkkäinen
    posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 17:15:03 as **
  • Finding motifs using random projections
    (2001), pp. 69-76.
    by Jeremy Buhler, Martin Tompa
    posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 17:14:38 as ** along with 1 person RamuAnandakrishnan
  • Designing seeds for similarity search in genomic DNA
    J. Comput. Syst. Sci., Vol. 70, No. 3. (May 2005), pp. 342-363.
    by Jeremy Buhler, Uri Keich, Yanni Sun
    posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 17:13:53 as **
  • Provably sensitive Indexing strategies for biosequence similarity search
    (2002), pp. 90-99.
    by Jeremy Buhler
    posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 17:13:17 as **
  • Efficient large-scale sequence comparison by locality-sensitive hashing
    Bioinformatics, Vol. 17, No. 5. (1 May 2001), pp. 419-428.
    by Jeremy Buhler
    posted to gapped-seeds sequence-alignment string-indexing string-matching by nedwards on 2007-08-14 17:12:49 as ** along with 1 person RamuAnandakrishnan
  • Vector seeds: an extension to spaced seeds
    J. Comput. Syst. Sci., Vol. 70, No. 3. (May 2005), pp. 364-380.
    by Brona Brejová, Daniel G Brown, Tomás Vinar
    posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 17:09:59 as **
  • Optimal spaced seeds for faster approximate string matching
    Journal of Computer and System Sciences, Vol. 73, No. 7. (November 2007), pp. 1035-1044.
    by Martin Farach-Colton, Gad M Landau, Cenk S Sahinalp, Dekel Tsur
    posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 15:54:01 as ** along with 1 person and 1 group AbnerCYH CSBBGraphTheory
  • Superiority and complexity of the spaced seeds
    (2006), pp. 444-453.
    by Ming Li, Bin Ma, Louxin Zhang
    posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 15:53:17 as ** along with 1 person treangen
  • Improved hit criteria for DNA local alignment.
    BMC Bioinformatics, Vol. 5 (14 October 2004)
    by L Noé, G Kucherov
    posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 15:51:28 as ** along with 4 people treangen bozdagd AaronDarling timflutre
  • A tutorial of recent developments in the seeding of local alignment.
    J Bioinform Comput Biol, Vol. 2, No. 4. (December 2004), pp. 819-842.
    by DG Brown, M Li, B Ma
    posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 15:48:09 as ** along with 1 person and 2 groups barry structural_bioinformatics Bioinformatics
  • A unifying framework for seed sensitivity and its application to subset seeds.
    J Bioinform Comput Biol, Vol. 4, No. 2. (April 2006), pp. 553-569.
    by G Kucherov, L Noé, M Roytberg
    posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 15:47:43 as **
  • Choosing the best heuristic for seeded alignment of DNA sequences.
    BMC Bioinformatics, Vol. 7, No. 1. (13 March 2006)
    by Yanni Sun, Jeremy Buhler
    posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 15:47:12 as ** along with 1 person eckart_bindewald
  • Indel seeds for homology search.
    Bioinformatics, Vol. 22, No. 14. (15 July 2006)
    by D Mak, Y Gelfand, G Benson
    posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 15:46:57 as **
  • Good spaced seeds for homology search.
    Bioinformatics, Vol. 20, No. 7. (1 May 2004), pp. 1053-1059.
    by KP Choi, F Zeng, L Zhang
    posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 15:46:43 as **
  • Designing multiple simultaneous seeds for DNA similarity search.
    J Comput Biol, Vol. 12, No. 6. (g 2005), pp. 847-861.
    by Y Sun, J Buhler
    posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 15:46:09 as ** along with 2 people nuke2005 treangen
  • Optimizing multiple spaced seeds for homology search.
    J Comput Biol, Vol. 13, No. 7. (September 2006), pp. 1355-1368.
    by J Xu, D Brown, M Li, B Ma
    posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 15:45:56 as **
  • Quick, practical selection of effective seeds for homology search.
    J Comput Biol, Vol. 12, No. 9. (November 2005), pp. 1137-1152.
    by FP Preparata, L Zhang, KP Choi
    posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 15:45:34 as **
  • Optimal spaced seeds for homologous coding regions.
    J Bioinform Comput Biol, Vol. 1, No. 4. (January 2004), pp. 595-610.
    by B Brejová, DG Brown, T Vinar
    posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 15:45:07 as **
  • Designing sensitive and specific spaced seeds for cross-species mRNA-to-genome alignment.
    J Comput Biol, Vol. 14, No. 2. (March 2007), pp. 113-130.
    by L Zhou, L Florea
    posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 15:44:46 as ** along with 1 person jyuh
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