nedwards's sequence-alignment [46 articles] Export Sort

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	Multiple spaced seeds for homology search [My Copy] Bioinformatics, Vol. 23, No. 22. (15 November 2007), pp. 2969-2977. 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 4 people n00c dfdong treangen cjeans
	Effect of the mutation rate and background size on the quality of pathogen identification [My Copy] Bioinformatics, Vol. 23, No. 20. (19 September 2007), pp. btm420-2671. by Chris Reed, Viacheslav Fofanov, Catherine Putonti, Sergei Chumakov, Tom Slezak, Yuriy Fofanov posted to dna-based microorganism-identification sequence-alignment string-indexing string-matching by nedwards on 2007-12-14 17:02:58 as along with 1 person druvus
	High-throughput sequence alignment using Graphics Processing Units [My Copy] BMC Bioinformatics, Vol. 8, No. 1. (2007), 474. by Michael Schatz, Cole Trapnell, Arthur Delcher, Amitabh Varshney posted to sequence-alignment string-matching by nedwards on 2007-12-13 14:38:34 as along with 21 people and 3 groups agbiotec cthachuk aheilbut druvus polivares naoya n00c natstreet rschulz operon orzenil Yanno guhjy sephy lusk laughcry mdimon cndewey heliopais urgi tpreeprem BergmanLab KCL & UCL Bioinformatics gatech-compgenomics
	Generalized correlation functions and their applications in selection of optimal multiple spaced seeds for homology search. [My Copy] 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 [My Copy] 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 along with 1 person n00c
	High-throughput identification of proteins and unanticipated sequence modifications using a mass-based alignment algorithm for MS/MS de novo sequencing results. [My Copy] Anal Chem, Vol. 76, No. 8. (15 April 2004), pp. 2220-2230. by B. C. Searle, S. Dasari, M. Turner, et al.A. P. Reddy, D. Choi, P. A. Wilmarth, A. L. McCormack, L. L. David, S. R. Nagalla posted to denovo-interpretation peptide-identification proteomics sequence-alignment tandem-mass-spectrometry by nedwards on 2007-08-30 16:26:09 as
	Space-efficient whole genome comparisons with Burrows-Wheeler transforms. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 12, No. 4. (May 2005), pp. 407-415. by Ross A. Lippert posted to burrows-wheeler seed-strategies sequence-alignment string-indexing string-matching by nedwards on 2007-08-30 16:08:16 as along with 3 people and 1 group polivares n00c antonkratz BergmanLab
	Algorithms on strings, trees, and sequences : computer science and computational biology [My Copy] (15 January 2007) by Dan Gusfield posted to inexact-string-matching sequence-alignment string-indexing string-matching suffix-trees by nedwards on 2007-08-22 14:20:28 as along with 20 people and 2 groups abergeron n00c stharward enricos Scis0000002 Neeperando mircea renewang timflutre ujh creswick tijl grzegorz luispedro emranmohdtamil hoangmit thonnardo pool007 ep161302 reyez Centre de Recherches Interdisciplinaires Pattern-Analysis
	PatternHunter: faster and more sensitive homology search [My Copy] Bioinformatics, Vol. 18, No. 3. (1 March 2002), pp. 440-445. by Bin Ma, John Tromp, Ming 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 11 people n00c druvus maria_hauser mmartin umit nuke2005 catmat treangen natstreet DickSilver bozdagd
	The Intronerator: exploring introns and alternative splicing in Caenorhabditis elegans [My Copy] Nucl. Acids Res., Vol. 28, No. 1. (1 January 2000), pp. 91-93. by James W. Kent, Alan M. Zahler posted to alignment-anchors seed-strategies sequence-alignment string-indexing by nedwards on 2007-08-17 18:39:58 as along with 2 people and 1 group thegoose2 tharris C. elegans / WormBase
	Human–Mouse Alignments with BLASTZ [My Copy] Genome Research, Vol. 13, No. 1. (1 January 2003), pp. 103-107. by Scott Schwartz, W. James Kent, Arian Smit, et al.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 6 people and 1 group gdb daveGerrard druvus operon indigoviolet treangen EisenLab
	A Space-Efficient Construction of the Burrows-Wheeler Transform for Genomic Data [My Copy] Journal of Computational Biology, Vol. 12, No. 7. (September 2005), pp. 943-951. by Ross .. Lippert,, Clark .. Mobarry,, Brian .. Walenz, posted to burrows-wheeler seed-strategies sequence-alignment string-indexing by nedwards on 2007-08-17 15:04:15 as along with 4 people lianping n00c antonkratz dleinhaeuser
	Finding anchors for genomic sequence comparison [My Copy] In RECOMB '04: Proceedings of the eighth annual international conference on Resaerch in computational molecular biology (2004), pp. 233-241. by Ross A. Lippert, Xiaoyue Zhao, Liliana Florea, Clark Mobarry, Sorin Istrail posted to alignment-anchors seed-strategies sequence-alignment by nedwards on 2007-08-17 15:02:14 as
	Approximate Boyer-Moore string matching [My Copy] SIAM J. Comput., Vol. 22, No. 2. (April 1993), pp. 243-260. by Jorma Tarhio, Esko Ukkonen posted to inexact-string-matching sequence-alignment string-matching by nedwards on 2007-08-17 14:58:16 as
	Genome-wide selection of unique and valid oligonucleotides [My Copy] Nucleic Acids Research, Vol. 33, No. 13. (2005), pp. e115-e115. by Heikki Hyyro, Martti Juhola, Mauno Vihinen posted to oligonucleotide-design sequence-alignment unique-oligonucleotides by nedwards on 2007-08-17 14:53:07 as
	PROBEmer: a web-based software tool for selecting optimal DNA oligos [My Copy] Nucl. Acids Res., Vol. 31, No. 13. (1 July 2003), pp. 3746-3750. by Scott J. Emrich, Mary Lowe, Arthur L. Delcher posted to oligonucleotide-design sequence-alignment by nedwards on 2007-08-17 14:50:27 as
	OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach [My Copy] Nucl. Acids Res., Vol. 31, No. 12. (15 June 2003), pp. 3057-3062. by Jean-Marie Rouillard, Michael Zuker, Erdogan Gulari posted to oligonucleotide-design sequence-alignment by nedwards on 2007-08-17 14:49:49 as along with 5 people guxiyou stsaft malcook cthachuk yoanjacquemin
	Reducing the space requirement of suffix trees [My Copy] Software: Practice and Experience, Vol. 29, No. 13. (November 1999), pp. 1149-1171. by Stefan Kurtz posted to sequence-alignment string-indexing suffix-trees by nedwards on 2007-08-17 14:46:20 as along with 3 people n00c dleinhaeuser ep161302
	Efficient Methods for Generating Optimal Single and Multiple Spaced Seeds [My Copy] In BIBE '04: Proceedings of the 4th IEEE Symposium on Bioinformatics and Bioengineering (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 [My Copy] 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 [My Copy] In RECOMB '04: Proceedings of the eighth annual international conference on Resaerch in computational molecular biology (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 [My Copy] Combinatorial Pattern Matching In 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 along with 2 people n00c mmartin
	On the complexity of the spaced seeds☆ [My Copy] Journal of Computer and System Sciences, Vol. 73, No. 7. (November 2007), pp. 1024-1034. by B MA,, M LI, posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 17:20:54 as along with 1 person n00c
	Multiseed Lossless Filtration [My Copy] 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 2 people treangen AaronDarling
	tPatternHunter: gapped, fast and sensitive translated homology search. [My Copy] Bioinformatics (Oxford, England), 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 along with 1 person maria_hauser
	FLASH: A Fast Look-Up Algorithm for String Homology [My Copy] In Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology (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 [My Copy] 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 along with 1 person mmartin
	Finding motifs using random projections [My Copy] In RECOMB '01: Proceedings of the fifth annual international conference on Computational biology (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 2 people RamuAnandakrishnan lptolik
	Designing seeds for similarity search in genomic DNA [My Copy] Journal of Computer and System Sciences, Vol. 70, No. 3. (May 2005), pp. 342-363. by J BUHLER,, U KEICH,, Y SUN, posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 17:13:53 as along with 1 person n00c
	Provably sensitive Indexing strategies for biosequence similarity search [My Copy] In RECOMB '02: Proceedings of the sixth annual international conference on Computational biology (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. [My Copy] Bioinformatics (Oxford, England), Vol. 17, No. 5. (1 May 2001), pp. 419-428. by J. Buhler posted to gapped-seeds sequence-alignment string-indexing string-matching by nedwards on 2007-08-14 17:12:49 as along with 2 people and 1 group ghattem RamuAnandakrishnan SIMR bioinformatics
	Vector seeds: An extension to spaced seeds [My Copy] Journal of Computer and System Sciences, Vol. 70, No. 3. (May 2005), pp. 364-380. by B BREJOVA,, D BROWN,, T VINAR, posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 17:09:59 as along with 1 person n00c
	Optimal spaced seeds for faster approximate string matching [My Copy] Journal of Computer and System Sciences In Bioinformatics III, 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 [My Copy] In SODA '06: Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm (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. [My Copy] 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 5 people umit AaronDarling timflutre bozdagd treangen
	Optimization techniques for string selection and comparison problems in genomics. Applying integer programming and heuristic algorithms for improved solutions. [My Copy] IEEE Eng Med Biol Mag, Vol. 24, No. 3. (n 2005), pp. 81-87. by C. N. Meneses, C. A. Oliveira, P. M. Pardalos posted to optimization sequence-alignment string-matching by nedwards on 2007-08-14 15:48:49 as
	A tutorial of recent developments in the seeding of local alignment. [My Copy] J Bioinform Comput Biol, Vol. 2, No. 4. (December 2004), pp. 819-842. by D. G. 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. [My Copy] 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. [My Copy] 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 [My Copy] Bioinformatics, Vol. 22, No. 14. (15 July 2006), pp. e341-349. by Denise Mak, Yevgeniy Gelfand, Gary Benson posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 15:46:57 as along with 1 person n00c
	Good spaced seeds for homology search [My Copy] Bioinformatics, Vol. 20, No. 7. (1 May 2004), pp. 1053-1059. by Kwok P. Choi, Fanfan Zeng, Louxin Zhang posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 15:46:43 as along with 1 person n00c
	Designing multiple simultaneous seeds for DNA similarity search. [My Copy] 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. [My Copy] 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. [My Copy] J Comput Biol, Vol. 12, No. 9. (November 2005), pp. 1137-1152. by F. P. Preparata, L. Zhang, K. P. 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. [My Copy] J Bioinform Comput Biol, Vol. 1, No. 4. (January 2004), pp. 595-610. by B. Brejová, D. G. 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. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 14, No. 2. (March 2007), pp. 113-130. by Leming Zhou, Liliana Florea posted to gapped-seeds sequence-alignment string-matching by nedwards on 2007-08-14 15:44:46 as along with 2 people lmzhou21 guhjy

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nedwards's sequence-alignment [46 articles] Export Sort

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