druvus's alignment [119 articles] Export

Recent papers added to druvus's library classified by the tag alignment. You can also see everyone's alignment.

	Sense from sequence reads: methods for alignment and assembly [My Copy] Nature Methods, Vol. 6, No. 11s. (15 October 2009), pp. S6-S12. by Paul Flicek, Ewan Birney posted to review next_generation assembly alignment by druvus on 2009-11-02 09:11:39 as along with 9 people Thaverkamp jasontsai natstreet seb1 chvlyl GeeSharpMinor n00c venancio desany
	MicroRazerS: Rapid alignment of small RNA reads [My Copy] Bioinformatics (29 October 2009), btp601. by Anne-Katrin Emde, Marcel Grunert, David Weese, Knut Reinert, Silke R. Sperling posted to rna-seq next_generation alignment by druvus on 2009-11-02 08:11:59 as along with 1 person heliopais
	FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix [My Copy] Mol Biol Evol, Vol. 26, No. 7. (1 July 2009), pp. 1641-1650. by Morgan N. Price, Paramvir S. Dehal, Adam P. Arkin posted to software evolution alignment by druvus on 2009-10-28 09:51:36 as along with 8 people and 2 groups houniao007 pyilmaz rneches djkt ppgardne jwm skembel nuin iSEEM Journal picks
	SeaView version 4 : a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. [My Copy] Molecular biology and evolution (23 October 2009), msp259. by Manolo Gouy, Stéphane Guindon, Olivier Gascuel posted to visualisation software next_generation alignment by druvus on 2009-10-26 07:46:59 as along with 1 person operon
	ABWGAT: Anchor Based Whole Genome Analysis Tool. [My Copy] Bioinformatics (14 October 2009), btp587. by Sarbashis Das, Anchal Vishnoi, Alok Bhattacharya posted to indel genome alignment by druvus on 2009-10-15 10:51:55 as along with 1 person natstreet
	Efficient Estimation of Pairwise Distances between Genomes [My Copy] Bioinformatics (13 October 2009), btp590. by Mirjana Domazet-Loso, Bernhard Haubold posted to genome distance alignment by druvus on 2009-10-14 09:04:02 as
	PLAST: parallel local alignment search tool for database comparison [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 329. by Van H. Nguyen, Dominique Lavenier posted to database alignment by druvus on 2009-10-12 16:41:17 as along with 4 people and 2 groups reyez polivares ppgardne installe BergmanLab Journal picks
	A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats [My Copy] IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 6, No. 2. (2009), pp. 180-189. by Todd J. Treangen, Aaron E. Darling, Guillaume Achaz, Mark A. Ragan, Xavier Messeguer, Eduardo P. C. Rocha posted to repeats alignment by druvus on 2009-10-06 16:03:01 as along with 1 person AaronDarling
	GRIL: genome rearrangement and inversion locator [My Copy] Bioinformatics, Vol. 20, No. 1. (1 January 2004), pp. 122-124. by Aaron E. Darling, Bob Mau, Frederick R. Blattner, Nicole T. Perna posted to genome alignment by druvus on 2009-10-06 15:56:50 as along with 4 people operon aprasad AaronDarling treangen
	Gapped Extension for Local Multiple Alignment of Interspersed DNA Repeats [My Copy] Bioinformatics Research and Applications (2008), pp. 74-86. by Todd Treangen, Aaron Darling, Mark Ragan, Xavier Messeguer posted to repeats alignment by druvus on 2009-10-06 15:49:13 as
	Functionally guided alignment of protein interaction networks for module detection. [My Copy] Bioinformatics (Oxford, England) (1 October 2009), btp569. by Waqar Ali, Charlotte M. Deane posted to proteome network alignment by druvus on 2009-10-02 08:47:11 as along with 1 person grahamc
	Reproducing the manual annotation of multiple sequence alignments using a SVM classifier [My Copy] Bioinformatics (21 September 2009), btp552. by Christian Blouin, Scott Perry, Allan Lavell, Edward Susko, Andrew J. Roger posted to svm alignment by druvus on 2009-09-22 09:04:15 as
	Computation and Analysis of Genomic Multi-Sequence Alignments [My Copy] Annual Review of Genomics and Human Genetics, Vol. 8, No. 1. (9 May 2007), pp. 193-213. by Mathieu Blanchette posted to sequence review alignment by druvus on 2009-08-31 14:24:26 as along with 7 people and 1 group natstreet treangen dpollard lilou nklee maximilianh aprasad EisenLab
	The many faces of sequence alignment [My Copy] Brief Bioinform, Vol. 6, No. 1. (1 January 2005), pp. 6-22. by Serafim Batzoglou posted to sequence alignment by druvus on 2009-08-31 14:21:40 as along with 11 people and 2 groups nuttpo n00c pimmy timflutre BioNica treangen balajis dpollard sdvillal gjuggler yoanjacquemin Bioinformatics EisenLab
	CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment [My Copy] BMC Bioinformatics, Vol. 9, No. Suppl 2. (2008), S10. by Svetlin Manavski, Giorgio Valle posted to sequence parallel alignment by druvus on 2009-08-17 10:02:49 as along with 9 people ihaque jmanning2k sterovetta operon alexgeorgiou antonkratz joule pansapiens bschaeli
	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 parallel alignment by druvus on 2009-08-17 10:00:51 as along with 19 people and 3 groups aheilbut polivares naoya n00c natstreet rschulz operon orzenil Yanno guhjy sephy lusk laughcry nedwards mdimon cndewey heliopais urgi tpreeprem BergmanLab KCL & UCL Bioinformatics gatech-compgenomics
	Is multiple-sequence alignment required for accurate inference of phylogeny? [My Copy] Systematic biology, Vol. 56, No. 2. (April 2007), pp. 206-221. by Michael Höhl, Mark A. Ragan posted to phylogeny alignment-free alignment by druvus on 2009-08-11 14:24:06 as along with 2 people treangen cjeans
	PineSAP--sequence alignment and SNP identification pipeline [My Copy] Bioinformatics, Vol. 25, No. 19. (1 October 2009), pp. 2609-2610. by Jill L. Wegrzyn, Jennifer M. Lee, John Liechty, David B. Neale posted to alignment pine pipeline plant snp by druvus on 2009-08-11 07:47:25 as along with 7 people jasontsai jsatkosk daforerog djkt operon nuin n00c
	Prokaryote phylogeny without sequence alignment: from avoidance signature to composition distance. [My Copy] Journal of bioinformatics and computational biology, Vol. 2, No. 1. (March 2004), pp. 1-19. by B. Hao, J. Qi posted to alignment bacteria phylogeny by druvus on 2009-08-10 15:32:21 as along with 1 person and 1 group skembel iSEEM
	Upcoming challenges for multiple sequence alignment methods in the high-throughput era [My Copy] Bioinformatics, Vol. 25, No. 19. (1 October 2009), pp. 2455-2465. by Carsten Kemena, Cedric Notredame posted to alignment next_generation by druvus on 2009-08-03 07:45:49 as along with 10 people and 2 groups fstrozzi manduca djkt rdiaz sjcockell torfinnnome walshtp nuin natstreet ollieredfernwork Journal picks Orengo Group Journal Picks
	Reordering contigs of draft genomes using the Mauve Aligner [My Copy] Bioinformatics, Vol. 25, No. 16. (15 August 2009), pp. 2071-2073. by Anna I. Rissman, Bob Mau, Bryan S. Biehl, Aaron E. Darling, Jeremy D. Glasner, Nicole T. Perna posted to alignment genome software by druvus on 2009-06-11 08:45:17 as along with 2 people and 1 group azazello natstreet Journal picks
	Fast Statistical Alignment [My Copy] PLoS Comput Biol, Vol. 5, No. 5. (29 May 2009), e1000392. by Robert K. Bradley, Adam Roberts, Michael Smoot, et al.Sudeep Juvekar, Jaeyoung Do, Colin Dewey, Ian Holmes, Lior Pachter posted to algorithm alignment by druvus on 2009-05-29 08:45:28 as along with 18 people and 1 group seb1 rdowell timflutre natstreet n00c yylin aprasad Gorzomagnificent guhjy dakelley reyez rec3141 farhat operon bmduggan nuin AlexBateman djkt Journal picks
	CORAL: aligning conserved core regions across domain families [My Copy] Bioinformatics, Vol. 25, No. 15. (1 August 2009), pp. 1862-1868. by Jessica H. Fong, Aron Marchler-Bauer posted to alignment clustering domain by druvus on 2009-05-27 08:40:15 as along with 3 people and 3 groups ollieredfernwork AlexBateman natstreet Orengo Group Journal Picks Journal picks iSEEM
	How to map billions of short reads onto genomes. [My Copy] Nature biotechnology, Vol. 27, No. 5. (May 2009), pp. 455-457. by Cole Trapnell, Steven L. Salzberg posted to alignment next_generation by druvus on 2009-05-14 11:25:30 as along with 22 people and 4 groups torfinnnome daforerog jonilaserson mkiyer Annab darian polivares ghattem kiekyon n00c GeeSharpMinor guhjy nuin reyez orzenil Thaverkamp natstreet fenghezi Stew inesdesantiago idonaldson neils Chinnaiyan Lab BergmanLab SIMR bioinformatics Bioinformatics - CRUK
	Sim4cc: a cross-species spliced alignment program. [My Copy] Nucleic acids research (8 May 2009) by Leming Zhou, Mihaela Pertea, Arthur L L. Delcher, Liliana Florea posted to alignment populus software by druvus on 2009-05-12 15:04:27 as along with 1 person natstreet
	ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 11. (1 June 2009), pp. 1424-1425. by You Jung J. Kim, Nikhil Teletia, Victor Ruotti, et al.Christopher A. Maher, Arul M. Chinnaiyan, Ron Stewart, James A. Thomson, Jignesh M. Patel posted to alignment mapping next_generation by druvus on 2009-05-05 15:26:53 as along with 11 people and 1 group mmartin n00c guhjy nuin idonaldson AlexBateman bmajoros humburg Thaverkamp svenrahmann djkt Journal picks
	SSALN: An alignment algorithm using structure-dependent substitution matrices and gap penalties learned from structurally aligned protein pairs [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 62, No. 4. (2006), pp. 881-891. by Jian Qiu, Ron Elber posted to alignment proteome software by druvus on 2009-03-30 16:33:27 as along with 1 person j3xucite
	A study on protein sequence alignment quality [My Copy] Proteins: Structure, Function, and Genetics, Vol. 46, No. 3. (2002), pp. 330-339. by Arne Elofsson posted to alignment sequence by druvus on 2009-03-30 16:31:43 as
	A probabilistic model of local sequence alignment that simplifies statistical significance estimation. [My Copy] PLoS computational biology, Vol. 4, No. 5. (30 May 2008), e1000069. by Sean R. Eddy posted to alignment hmm statistics by druvus on 2009-03-29 11:50:29 as along with 9 people cmzmasek vwchan treangen BioNica saerni dakelley aramesh2 Ema gdb
	Infernal 1.0: inference of RNA alignments. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 10. (15 May 2009), pp. 1335-1337. by Eric P. Nawrocki, Diana L. Kolbe, Sean R. Eddy posted to alignment rna software by druvus on 2009-03-24 08:35:23 as along with 6 people and 1 group reyez operon djkt neils nuin natstreet iSEEM
	Alignment and Prediction of cis-Regulatory Modules Based on a Probabilistic Model of Evolution [My Copy] PLoS Comput Biol, Vol. 5, No. 3. (13 March 2009), e1000299. by Xin He, Xu Ling, Saurabh Sinha posted to alignment cis evolution predictions tf by druvus on 2009-03-13 11:59:05 as along with 9 people roys megraw lusk TRHvidsten kieran101 nuin djkt mhamada maximilianh
	Distribution and intensity of constraint in mammalian genomic sequence. [My Copy] Genome Res, Vol. 15, No. 7. (July 2005), pp. 901-913. by G. M. Cooper, E. A. Stone, G. Asimenos, E. D. Green, S. Batzoglou, A. Sidow posted to alignment proteome by druvus on 2009-03-04 15:39:04 as along with 6 people operon aprasad nirfriedman JeffR100 Garamonfok tale
	Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity [My Copy] Genome Research, Vol. 15, No. 7. (July 2005), pp. 978-986. by Eric A. Stone, Arend Sidow posted to alignment classification proteome by druvus on 2009-03-04 15:37:18 as along with 1 person jessopher
	Empirical profile mixture models for phylogenetic reconstruction. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 20. (15 October 2008), pp. 2317-2323. by l. e. . S. Quang, O. Gascuel, N. Lartillot posted to algorithm alignment likelihood by druvus on 2009-03-04 12:40:11 as along with 1 person nuin
	Phylogenetic mixture models for proteins [My Copy] Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 363, No. 1512. (27 December 2008), pp. 3965-3976. by Si Q. Le, Nicolas Lartillot, Olivier Gascuel posted to alignment proteome by druvus on 2009-03-04 12:38:56 as along with 1 person operon
	An improved general amino acid replacement matrix. [My Copy] Molecular biology and evolution, Vol. 25, No. 7. (1 July 2008), pp. 1307-1320. by Si Quang Q. Le, Olivier Gascuel posted to algorithm alignment likelihood by druvus on 2009-03-04 12:34:54 as along with 5 people and 1 group BioNica lizbiogen stajich friendpine dmp Mycology
	A topological transformation in evolutionary tree search methods based on maximum likelihood combining p-ECR and neighbor joining [My Copy] BMC Bioinformatics, Vol. 9, No. Suppl 6. (2008) by Mao Z. Guo, Jian F. Li, Yang Liu posted to algorithm alignment likelihood by druvus on 2009-03-04 12:29:53 as
	Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood [My Copy] Bioinformatics, Vol. 21, No. 24. (15 December 2005), pp. 4338-4347. by Wim Hordijk, Olivier Gascuel posted to algorithm alignment likelihood software by druvus on 2009-03-04 12:27:39 as
	Approximate Likelihood-Ratio Test for Branches: A Fast, Accurate, and Powerful Alternative [My Copy] Systematic Biology, Vol. 55, No. 4. (August 2006), pp. 539-552. by Anisimova, Maria, Gascuel, Olivier posted to alignment likelihood phylogeny by druvus on 2009-03-04 12:22:36 as along with 2 people polpotak redelings
	Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. [My Copy] Genome research, Vol. 18, No. 11. (10 November 2008), pp. 1814-1828. by Benedict Paten, Javier Herrero, Kathryn Beal, Stephen Fitzgerald, Ewan Birney posted to alignment paralog by druvus on 2009-01-08 10:25:08 as along with 8 people gdb mhamada natstreet davfre rschulz treangen Neeperando gjuggler
	The meaning of alignment: lessons from structural diversity [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008) by Walter Pirovano, Anton K. Feenstra, Jaap Heringa posted to alignment proteome structure by druvus on 2008-12-29 10:41:18 as along with 13 people pimmy swtimmer dimka mhamada reyez treangen markusd j3xucite nuin kshameer chad_davis taguchi pansapiens
	DNA reference alignment benchmarks based on tertiary structure of encoded proteins [My Copy] Bioinformatics, Vol. 23, No. 19. (1 October 2007), pp. 2648-2649. by Hyrum Carroll, Wesley Beckstead, Timothy O'Connor, et al.Mark Ebbert, Mark Clement, Quinn Snell, David Mcclellan posted to alignment review software by druvus on 2008-12-19 15:38:07 as along with 1 person niallhaslam
	An enhanced RNA alignment benchmark for sequence alignment programs [My Copy] Algorithms for Molecular Biology, Vol. 1, No. 1. (24 October 2006), 19. by Andreas Wilm, Indra Mainz, Gerhard Steger posted to alignment review software by druvus on 2008-12-19 15:36:56 as along with 2 people nuin dquest
	The iRMSD: a local measure of sequence alignment accuracy using structural information. [My Copy] Bioinformatics, Vol. 22, No. 14. (15 July 2006) by F. Armougom, S. Moretti, V. Keduas, C. Notredame posted to alignment software by druvus on 2008-12-19 15:36:35 as along with 1 person chad_davis
	MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information [My Copy] Nucleic Acids Research, Vol. 34, No. 16. (September 2006), pp. 4364-4374. by Pei, Jimin, Grishin, V. Nick posted to alignment markov software by druvus on 2008-12-19 15:35:00 as along with 2 people natstreet operon
	MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. [My Copy] Nucleic acids research, Vol. 30, No. 14. (15 July 2002), pp. 3059-3066. by Kazutaka Katoh, Kazuharu Misawa, Kei-ichi Kuma, Takashi Miyata posted to alignment software by druvus on 2008-12-19 15:31:41 as along with 8 people biomcgary calderonv natstreet treangen rabio timflutre marti urgi
	MAFFT version 5: improvement in accuracy of multiple sequence alignment. [My Copy] Nucleic acids research, Vol. 33, No. 2. (2005), pp. 511-518. by K. Katoh, K. Kuma, H. Toh, T. Miyata posted to alignment software by druvus on 2008-12-19 15:31:18 as along with 8 people and 1 group hryk BioNica treangen CharlesM caporaso rabio timflutre urgi biomedical-nlp
	Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework [My Copy] BMC Bioinformatics, Vol. 9 (25 April 2008), 212. by Kazutaka Katoh, Hiroyuki Toh posted to alignment software by druvus on 2008-12-19 15:29:52 as along with 1 person elfar
	MView: a web-compatible database search or multiple alignment viewer. [My Copy] Bioinformatics (Oxford, England), Vol. 14, No. 4. (1998), pp. 380-381. by N. P. Brown, C. Leroy, C. Sander posted to alignment visualisation by druvus on 2008-12-19 15:27:12 as along with 1 person natstreet
	Ngila: global pairwise alignments with logarithmic and affine gap costs. [My Copy] Bioinformatics (Oxford, England), Vol. 23, No. 11. (1 June 2007), pp. 1427-1428. by R. A. Cartwright posted to alignment indel software by druvus on 2008-12-17 15:01:57 as along with 2 people timflutre bozdagd

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genome	390
software	375
evolution	279
phylogeny	270
statistics	221
review	211
bacteria	188
database	173
francisella	162
proteome	160
repeat	158
next_generation	149
plant	140
tandem	124
alignment	119
marker	106
network	104
annotation	99
semantic	97
wms	95
bioinformatics	90
population	89
comperative_genomics	82
tf	81
sequence	79
populus	71
mirna	69
gene	66
genetics	66
algorithm	60
classification	58
visualisation	58
snp	57
assembly	55
microarray	54
pathogen	53
arabidopsis	52
r	51
web_20	51
sequencing	49
est	47
pipeline	47
predictions	44
mapping	40
genetic	39
pcr	39
synthetic_biology	38
indel	37
model	36
distance	35
ecoli	35
mutation	35
454	34
likelihood	33
ortholog	33
taverna	33
motif	32
metagenomics	31
ontology	30
references	30
wiki	30
coalescent	29
family	29
bayesian	28
rice	27
clustering	26
browser	25
simulation	25
ssr	25
expression	23
microbial_forensics	23
biodefense	22
domain	21
synteny	21
tom	21
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srna	20
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gmod	19
duplication	18
mycobacterium	18
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target	18
bacillus	17
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promoter	16
book	15
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multivariate	15
primer	14
virulence	14
blast	13
comment	13
environmental	13
prokaryote	13
vntr	13
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geography	12
hmm	12
ricinus	12
semantic_web	12
solexa	12
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binding	11
datasharing	11
development	11
human	11
mitocondria	11
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anthrax	10
cis	10
drosophila	10
eukaryote	10
mvla	10
pangenome	10
parallel	10
pubmed	10
repeats	10
clostridium	9
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das	9
module	9
spatial	9
virus	9
writing	9
bioconductor	8
grid	8
indels	8
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rdf	8
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systems_biology	8
web_service	8
alignment-free	7
biomoby	7
consensus	7
coxiella	7
forensics	7
illumina	7
insilico	7
island	7
ncrna	7
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pestis	7
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yeast	7
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php	3
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splicing	3
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uorf	3
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chado	2
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cotton	2
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kegg	2
kernel	2
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linkage_disequilibrium	2
linux	2
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meta-analysis	2
metapopulation	2
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ontologies	2
owl	2
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affymetrix	1
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anthocyanin	1
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tularensis	1
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validation	1
viewer	1
visualsisation	1
wgcna	1
wheat	1
wolbachia	1

druvus's alignment [119 articles] Export

druvus's tags