BioNica's alignment [67 articles] Export

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

	A comparison of scoring functions for protein sequence profile alignment [My Copy] Bioinformatics, Vol. 20, No. 8. (22 May 2004), pp. 1301-1308. by R. C. Edgar, K. Sjolander posted to alignment method by BioNica on 2009-07-19 20:32:26 as along with 1 person danatcaret
	Divide-and-Conquer Multiple Sequence Alignment [My Copy] No. 97-02. (1997) by J. Stoye posted to alignment dca method by BioNica on 2009-05-27 21:57:10 as
	A benchmark of multiple sequence alignment programs upon structural RNAs [My Copy] Nucleic Acids Research, Vol. 33, No. 8. (2005), pp. 2433-2439. by P. P. Gardner, A. Wilm, S. Washietl posted to alignment evaluation method by BioNica on 2009-05-24 21:57:41 as along with 2 people arcticrasta ilh
	Analysis and comparison of benchmarks for multiple sequence alignment. [My Copy] In silico biology, Vol. 6, No. 4. (2006), pp. 321-339. by G. Blackshields, I. M. Wallace, M. Larkin, D. G. Higgins posted to alignment evaluation method by BioNica on 2009-05-24 21:41:46 as
	Evaluation measures of multiple sequence alignments. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 7, No. 1-2. (r 2000), pp. 261-276. by G. H. Gonnet, C. Korostensky, S. Benner posted to alignment method by BioNica on 2009-05-24 21:32:57 as
	A weighting system and algorithm for aligning many phylogenetically related sequences. [My Copy] Computer applications in the biosciences : CABIOS, Vol. 11, No. 5. (October 1995), pp. 543-551. by O. Gotoh posted to alignment method by BioNica on 2009-05-24 21:26:47 as
	MUSCLE: a multiple sequence alignment method with reduced time and space complexity [My Copy] BMC Bioinformatics, Vol. 5, No. 1. (19 August 2004), 113. by Robert Edgar posted to alignment method by BioNica on 2009-05-19 15:13:59 as along with 29 people and 5 groups rneches gwallau OscarLopez ivanffcc Helenita Joaquin kmma13 khlevy Pal tomjad mgomes hryk natstreet Md_2007 sebk wallacei knaseanka chrn jwm balajis gbart caporaso sriram_s cdallett sanchezbuelna timflutre gisle urgi Ema LabDros References for 3DSim paper Radiation_Damage Stressosome biomedical-nlp
	Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features. [My Copy] Nucleic acids research, Vol. 37, No. 3. (22 February 2009), pp. 858-865. by T. Lassmann, O. Frings, E. L. L. Sonnhammer posted to alignment method by BioNica on 2009-05-19 14:42:42 as along with 4 people maria_hauser robfsouza guhjy nuin
	DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment [My Copy] BMC Bioinformatics, Vol. 6, No. 1. (2005), 66. by A. R. Subramanian, J. Weyer-Menkhoff, M. Kaufmann, B. Morgenstern posted to alignment method by BioNica on 2009-05-19 14:38:22 as along with 3 people walshtp treangen moborg
	DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment [My Copy] Algorithms for molecular biology : AMB, Vol. 3, No. 1. (27 May 2008), 6. by A. R. Subramanian, M. Kaufmann, B. Morgenstern posted to alignment method by BioNica on 2009-05-19 14:32:52 as along with 7 people Copper_Calcio walshtp druvus treangen operon reyez dquest
	DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment [My Copy] Bioinformatics, Vol. 15, No. 3. (1 March 1999), pp. 211-218. by B. Morgenstern posted to alignment method by BioNica on 2009-05-19 14:29:19 as along with 1 person chad_davis
	Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment. [My Copy] Nucleic acids research, Vol. 34, No. Web Server issue. (1 July 2006) by Timo Lassmann, Erik L. Sonnhammer posted to alignment evaluation method by BioNica on 2009-05-19 14:19:13 as along with 2 people orzenil Haggan
	Weights for data related by a tree. [My Copy] J Mol Biol, Vol. 207, No. 4. (20 June 1989), pp. 647-653. by S. F. Altschul, R. J. Carroll, D. J. Lipman posted to alignment method by BioNica on 2009-05-12 23:55:55 as along with 3 people and 1 group souravc nuke2005 newton1234 iSEEM
	The Multiple Sequence Alignment Problem in Biology [My Copy] SIAM Journal on Applied Mathematics, Vol. 48, No. 5. (1988), pp. 1073-1082. by H. Carrillo, D. Lipman posted to alignment method msa by BioNica on 2009-05-12 23:39:34 as
	Multiple DNA and protein sequence alignment based on segment-to-segment comparison [My Copy] Proceedings of the National Academy of Sciences, Vol. 93, No. 22. (29 October 1996), pp. 12098-12103. by B. Morgenstern, A. Dress, T. Werner posted to alignment method by BioNica on 2009-05-11 19:47:28 as along with 3 people adijr gjuggler newton1234
	Multiple sequence alignment with the divide-and-conquer method [My Copy] Gene, Vol. 211, No. 2. (12 May 1998), pp. GC45-GC56. by J. Stoye posted to alignment dca method by BioNica on 2009-05-11 19:36:46 as
	A general method for fast multiple sequence alignment. [My Copy] Gene, Vol. 172, No. 1. (12 June 1996) by U. Tönges, S. W. Perrey, J. Stoye, A. W. Dress posted to alignment dca method by BioNica on 2009-05-11 19:21:30 as
	DCA: an efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment. [My Copy] Computer applications in the biosciences : CABIOS, Vol. 13, No. 6. (December 1997), pp. 625-626. by J. Stoye, V. Moulton, A. W. Dress posted to alignment dca method by BioNica on 2009-05-11 19:19:01 as
	DIALIGN: finding local similarities by multiple sequence alignment [My Copy] Bioinformatics, Vol. 14, No. 3. (1 April 1998), pp. 290-294. by B. Morgenstern, K. Frech, A. Dress, T. Werner posted to alignment method by BioNica on 2009-05-11 19:00:42 as along with 2 people and 1 group indigoviolet adijr EisenLab
	A statistical score for assessing the quality of multiple sequence alignments. [My Copy] BMC bioinformatics, Vol. 7 (03 November 2006), 484. by V. Ahola, T. Aittokallio, M. Vihinen, E. Uusipaikka posted to alignment evaluation by BioNica on 2009-05-07 16:13:53 as along with 3 people nuin druvus treangen
	Segment-based multiple sequence alignment [My Copy] Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i187-192. by T. Rausch, A. K. Emde, D. Weese, A. Doring, C. Notredame, K. Reinert posted to alignment method by BioNica on 2009-05-07 15:05:57 as along with 9 people nuin darian Md_2007 zwang Ema APRegier djkt aprasad groepl
	Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment [My Copy] Bioinformatics (4 December 2008), btn630. by B. Paten, J. Herrero, K. Beal, E. Birney posted to alignment method by BioNica on 2009-05-04 19:11:01 as along with 9 people guhjy dakelley semrich gjuggler djkt rschulz birney operon druvus
	A general method applicable to the search for similarities in the amino acid sequence of two proteins. [My Copy] Journal of molecular biology, Vol. 48, No. 3. (March 1970), pp. 443-453. by S. B. Needleman, C. D. Wunsch posted to alignment classics method by BioNica on 2009-04-22 18:38:55 as along with 16 people windman83 esyoun stsaft timflutre mcbla db344 DarkMars cawelsh9 sebk jwm dgront rabio incovoma yylin newton1234 Ema
	Progressive sequence alignment as a prerequisite to correct phylogenetic trees. [My Copy] J Mol Evol, Vol. 25, No. 4. (1987), pp. 351-360. by D. F. Feng, R. F. Doolittle posted to alignment method by BioNica on 2009-04-22 17:48:25 as along with 5 people esyoun balajis nuke2005 AaronDarling newton1234
	Kalign--an accurate and fast multiple sequence alignment algorithm. [My Copy] BMC bioinformatics, Vol. 6 (2005) by T. Lassmann, E. L. Sonnhammer posted to alignment method by BioNica on 2009-04-22 17:44:43 as along with 7 people maria_hauser Thaverkamp johanviklund aalibes CharlesM knaseanka Haggan
	The limits of protein sequence comparison? [My Copy] Current opinion in structural biology, Vol. 15, No. 3. (June 2005), pp. 254-260. by William R. Pearson, Michael L. Sierk posted to alignment by BioNica on 2009-04-16 21:41:55 as along with 3 people and 1 group svozil richardbickerton yylin Bioinformatics
	Multiple sequence alignment using ClustalW and ClustalX. [My Copy] Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.], Vol. Chapter 2 (August 2002) by J. D. Thompson, T. J. Gibson, D. G. Higgins posted to alignment by BioNica on 2009-04-16 16:41:04 as along with 1 person Lombardo_7
	CLUSTAL: a package for performing multiple sequence alignment on a microcomputer [My Copy] Gene, Vol. 73, No. 1. (15 December 1988), pp. 237-244. by Desmond G. Higgins, Paul M. Sharp posted to alignment by BioNica on 2009-04-16 16:40:08 as along with 3 people Lombardo_7 moborg AbnerCYH
	Clustal W and Clustal X version 2.0 [My Copy] Bioinformatics, Vol. 23, No. 21. (1 November 2007), pp. 2947-2948. by M. A. Larkin, G. Blackshields, N. P. Brown, et al.R. Chenna, P. A. McGettigan, H. McWilliam, F. Valentin, I. M. Wallace, A. Wilm, R. Lopez, J. D. Thompson, T. J. Gibson, D. G. Higgins posted to alignment by BioNica on 2009-04-16 16:39:11 as along with 18 people l00cas vprieto Copper_Calcio TLVincent tomjad udivi Keksle hpm druvus treangen jwm cassj lisa1 ryanraaum bmaust alanrw mschofie marck
	Multiple sequence alignment with the Clustal series of programs [My Copy] Nucl. Acids Res., Vol. 31, No. 13. (1 July 2003), pp. 3497-3500. by Ramu Chenna, Hideaki Sugawara, Tadashi Koike, et al.Rodrigo Lopez, Toby J. Gibson, Desmond G. Higgins, Julie D. Thompson posted to alignment by BioNica on 2009-04-16 16:38:35 as along with 8 people and 1 group vprieto Lombardo_7 miguel chad_davis beatrizfernandez raylim xingxu marck Microbial-Ecology
	Using CLUSTAL for multiple sequence alignments. [My Copy] Methods Enzymol, Vol. 266 (1996), pp. 383-402. by D. G. Higgins, J. D. Thompson, T. J. Gibson posted to alignment by BioNica on 2009-04-16 16:37:05 as along with 3 people Lombardo_7 jtomasch mschofie
	Multiple sequence alignments [My Copy] Current Opinion in Structural Biology, Vol. 15, No. 3. (June 2005), pp. 261-266. by I. M. Wallace, G. Blackshields, D. G. Higgins posted to alignment method by BioNica on 2009-04-15 22:31:07 as along with 5 people Thaverkamp martainn mdimmic bpb nklee
	Recent Evolutions of Multiple Sequence Alignment Algorithms [My Copy] PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e123. by C. Notredame posted to alignment method by BioNica on 2009-04-15 22:25:48 as along with 9 people and 1 group treangen natstreet druvus giovenko agustinarce skhadar sobolevnrm hpaces mingzhi baker-group
	PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments. [My Copy] Nucleic acids research, Vol. 34, No. Web Server issue. (1 July 2006) by S. Moretti, F. Reinier, O. Poirot, et al.F. Armougom, S. Audic, V. Keduas, C. Notredame posted to alignment codon method programs protein by BioNica on 2009-03-15 02:25:53 as
	Quality assessment of multiple alignment programs. [My Copy] FEBS Lett, Vol. 529, No. 1. (2 October 2002), pp. 126-130. by T. Lassmann, E. L. Sonnhammer posted to alignment method by BioNica on 2009-03-14 22:09:34 as along with 2 people knaseanka major724
	Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems. [My Copy] Bioinformatics, Vol. 20, No. 10. (10 July 2004), pp. 1546-1556. by C. Grasso, C. Lee posted to alignment method by BioNica on 2009-03-14 21:18:10 as along with 4 people Neeperando scis0000001 treangen AbnerCYH
	T-Coffee: A novel method for fast and accurate multiple sequence alignment. [My Copy] Journal of molecular biology, Vol. 302, No. 1. (8 September 2000), pp. 205-217. by C. Notredame, D. G. Higgins, J. Heringa posted to alignment method by BioNica on 2009-03-04 17:45:01 as along with 17 people and 1 group bratwurst viktor21614 tomjad robert laurabailey medic0747 sebk miguel dayjm indigoviolet ffranca treangen Haggan siebertm adijr marti newton1234 EisenLab
	M-Coffee: combining multiple sequence alignment methods with T-Coffee [My Copy] Nucleic Acids Research, Vol. 34, No. 6. (2006), pp. 1692-1699. by I. M. Wallace, O. O'Sullivan, D. G. Higgins, C. Notredame posted to alignment method by BioNica on 2009-03-04 17:38:24 as along with 2 people and 2 groups gjuggler marcius BioinfoCIPF SGU-CIPF
	Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis [My Copy] Science, Vol. 320, No. 5883. (20 June 2008), pp. 1632-1635. by Ari Loytynoja, Nick Goldman posted to alignment method by BioNica on 2009-02-03 17:42:01 as along with 29 people and 3 groups memerman operon TRHvidsten cmzmasek timflutre pradiptaray alexeid marti bpcusack 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
	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 alignment by BioNica on 2009-02-03 17:31:08 as along with 11 people and 2 groups nuttpo druvus n00c pimmy timflutre treangen balajis dpollard sdvillal gjuggler yoanjacquemin Bioinformatics EisenLab
	From The Cover: An algorithm for progressive multiple alignment of sequences with insertions [My Copy] PNAS, Vol. 102, No. 30. (26 July 2005), pp. 10557-10562. by Ari Loytynoja, Nick Goldman posted to alignment method prank by BioNica on 2009-02-03 17:07:00 as along with 8 people and 1 group Thaverkamp federico_boschetti stevanspringer timflutre gjuggler hpaces dgront bpcusack FAB-lab
	ProbCons: Probabilistic consistency-based multiple sequence alignment. [My Copy] Genome Res, Vol. 15, No. 2. (February 2005), pp. 330-340. by C. B. Do, M. S. Mahabhashyam, M. Brudno, S. Batzoglou posted to alignment method by BioNica on 2009-02-03 17:05:30 as along with 7 people and 1 group bpb radek balajis stajich olympos newton1234 gjuggler Mycology
	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 method by BioNica on 2009-02-03 17:03:00 as along with 8 people and 1 group hryk druvus treangen CharlesM caporaso rabio timflutre urgi biomedical-nlp
	MUSCLE: multiple sequence alignment with high accuracy and high throughput [My Copy] Nucl. Acids Res., Vol. 32, No. 5. (19 March 2004), pp. 1792-1797. by R. C. Edgar posted to alignment method by BioNica on 2009-02-03 17:02:15 as along with 29 people and 2 groups mgomes jeargle tomjad foxpowa esyoun natstreet dquest gjuggler edvin yylin treangen sebk agustinarce fhsantanna nachtalp bpb chrn jwm Haggan sanchezbuelna timflutre olympos martainn newton1234 skumagai bmaust sconlan dmp kcrawlik Radiation_Damage Stressosome
	Recent developments in the MAFFT multiple sequence alignment program. [My Copy] Briefings in bioinformatics (27 March 2008) by K. Katoh, H. Toh posted to alignment method by BioNica on 2009-02-03 16:38:46 as along with 3 people treangen urgi timflutre
	Mind the Gaps: Evidence of Bias in Estimates of Multiple Sequence Alignments. [My Copy] Mol Biol Evol (20 August 2007) by Tanya Golubchik, Michael J J. Wise, Simon Easteal, Lars S S. Jermiin posted to alignment method by BioNica on 2009-02-03 16:30:10 as along with 7 people natstreet treangen druvus zwang lilou dandaman caseybrown
	Multiple sequence alignment using partial order graphs [My Copy] Bioinformatics, Vol. 18, No. 3. (1 March 2002), pp. 452-464. by Christopher Lee, Catherine Grasso, Mark F. Sharlow posted to alignment method by BioNica on 2009-02-03 16:21:06 as along with 9 people and 3 groups pimmy treangen Neeperando ana Cortel AbnerCYH azazello wenhan gjuggler structural_bioinformatics Bioinformatics MBLAB
	The accuracy of several multiple sequence alignment programs for proteins [My Copy] BMC Bioinformatics, Vol. 7, No. 1. (24 October 2006), 471. by Paulo Nuin, Zhouzhi Wang, Elisabeth Tillier posted to alignment by BioNica on 2009-02-03 16:17:13 as along with 11 people torfinnnome natstreet daforerog druvus treangen winterschlaefer viktor21614 gjuggler tny plofje rabio
	PROMALS3D: a tool for multiple protein sequence and structure alignments [My Copy] Nucl. Acids Res. (20 February 2008), gkn072. by Jimin Pei, Bong-Hyun Kim, Nick V. Grishin posted to alignment method by BioNica on 2009-02-03 16:14:29 as along with 3 people and 1 group newton1234 sunhwan sobolevnrm baker-group
	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 by BioNica on 2008-11-17 18:26:50 as along with 9 people cmzmasek druvus vwchan treangen saerni dakelley aramesh2 Ema gdb

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method	84
alignment	67
evolution	64
pathogenesis-related	63
chitinases	61
model	35
plant	34
selection	34
phylogeny	30
pr04	30
pr12	30
database	25
pr03	25
defensin	23
protein	23
defense	22
antifungal	20
peroxidase	19
pr08	19
pr11	17
pr13	17
pr02	16
pr14	16
chitin-binding	15
duplication	15
pr09	15
pr17	15
expression	14
germin-like	14
glycoside_hydrolases	14
resistance	13
germin	12
phylogenetic	12
programs	12
codon	11
homology	11
oxalate-oxidase	11
paml	11
structure	11
hordeum	10
polyploidy	10
thionin	10
antimicrobial	9
hmm	9
pr10	9
triticum	9
pr05	8
pr06	8
proteins	8
classics	7
hevein	7
phylogenetics	7
pr01	7
pr15	7
pr16	7
bioinformatics	6
evaluation	6
family	6
modeling	6
plant-pathogen	6
plant-pathogenic	6
allergens	5
darwinian	5
dna	5
evolutionary	5
gene_code	5
glucanases	5
maximum_likelihood	5
positive	5
powdery_mildew	5
pr1	5
wound-inducible	5
adaptive	4
analyses	4
color	4
dca	4
pr	4
pr07	4
pr5	4
sar	4
simulations	4
solanum	4
zea	4
antibiotic	3
classification	3
gymnosperms	3
likelihood	3
molecular_evolution	3
mutation	3
oxidative_burst	3
speciation	3
synergy	3
bayes	2
bayesian	2
blast	2
bootstrap	2
darwin	2
discussion	2
disease	2
ferrofluids	2
infection	2
inhibitor	2
molecular	2
multigenic	2
njplot	2
peptide	2
phyml	2
r-genes	2
ros	2
signal_transduction	2
tree-puzzle	2
aphid	1
arabidopsis	1
at2g14610	1
at2g37130	1
bacteria	1
basic	1
capsicum	1
cdna	1
cross-linking	1
dnatagger	1
ecology	1
ecosystem	1
fungal	1
gene-fusion	1
genetic-mapping	1
hybrid	1
induced	1
induction	1
isr	1
leaf-gall	1
malus	1
metabolism	1
metaphors	1
msa	1
nbd-arc	1
nectarin	1
neurobiology	1
neutral	1
neutrality	1
nicotiana	1
non-neutral	1
pathogenicity	1
pepper	1
physcomitrella	1
physiology	1
plant-insect	1
pollen	1
powdery-mildew	1
pr18	1
prank	1
proteinase	1
proteinase-inhibitor	1
protein-coding	1
reconstruction	1
review	1
secretory	1
serine_protease	1
superoxide_dismutase	1
synonymous	1
systemic	1
tree-thinking	1
upgma	1
xylanase	1

BioNica's alignment [67 articles] Export

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