ライフサイエンスコーパス: multiple alignment

1 We name our method QOMA (Quasi-Optimal Multiple Alignment).

2 tions and deletions consistent with an input multiple alignment.

3 stic to estimate the significance of a local multiple alignment.

4 cance score for multiple segments of a local multiple alignment.

5 gnment and a progressive algorithm for final multiple alignment.

6 heavily towards the promising regions of the multiple alignment.

7 ding frame to be maintained in the resulting multiple alignment.

8 el generalization of the classic notion of a multiple alignment.

9 subsequent sequences, and a nucleotide-level multiple alignment.

10 hylogenetic relationships were identified by multiple alignment.

11 earches performed, not on the quality of the multiple alignment.

12 ent clustering, paralogue identification and multiple alignment.

13 e query sequence was well represented in the multiple alignment.

14 e standard progressive alignment approach to multiple alignment.

15 single matches are consistent with a partial multiple alignment.

16 nd then incorporates them into a progressive multiple alignment.

17 utilize explicitly evolutionary profiles and multiple alignments.

18 h between a query sequence and a database of multiple alignments.

19 are systematically tracked in the context of multiple alignments.

20 We extend the BLAST theory to multiple alignments.

21 le success developing statistical scores for multiple alignments.

22 sing a partial order graph representation of multiple alignments.

23 served transcription factor binding sites in multiple alignments.

24 hat combines SwissProt annotations with Pfam multiple alignments.

25 merging sequences or parts of sequences into multiple alignments.

26 d as an objective function for refinement of multiple alignments.

27 igned regions and will aid in improvement of multiple alignments.

28 ed by the difficulty of obtaining reasonable multiple alignments.

29 airwise alignments can be extended to making multiple alignments.

30 scores for patterns derived from any set of multiple alignments.

31 f the possible signals and ignore reads with multiple alignments.

32 alculated from the posterior distribution of multiple alignments.

33 nnealing approach for exploring the space of multiple alignments.

34 ting complete ancestral sequences from large multiple alignments.

35 It can identify 'orthologous' CRMs without multiple alignments.

36 y Pfam and SUPERFAMILY, curated ensembles of multiple alignments.

37 define a posterior distribution of possible multiple alignments.

38 We develop a multiple alignment algorithm for Bayesian inference in t

39 egrative patient sample classification and a multiple alignment algorithm is also introduced for iden

40 s might also arise from the imperfections in multiple alignment algorithms and thus indicate possible

41 relationships are known to pose a problem to multiple alignment algorithms and to impede comparative

42 By modifying existing multiple alignment algorithms to make use of horizontal

43 Measuring the accuracy of multiple alignment algorithms with reference to BAliBASE

44 Multiple alignments among genomes are becoming increasin

45 Here we present an integrated multiple alignment and 3D structure visualization progra

46 comparative genomics annotation (100-species multiple alignment and conservation) and a novel distrib

47 The most commonly used methods fix a single multiple alignment and consider only substitutions as ph

48 rithmic idea also leads to new approaches to multiple alignment and fragment assembly.

49 ch cannot be satisfactorily done using other multiple alignment and motif discovery algorithms.

50 Multiple alignment and phylogenetic analysis of the prot

51 he links model and implications for Bayesian multiple alignment and phylogenetic profiling.

52 By applying multiple alignment and sequence optimization steps, we d

53 Adding more distant homologs to a multiple alignment and thus increasing its diversity may

54 es were identified by their positions in the multiple alignment and were defined as any two introns o

55 b interface is provided to view the results, multiple alignments and 3D superimpositions of structure

56 sm among one or more DNA or protein sequence multiple alignments and additional unaligned sequences.

57 plications allow users to visualize and edit multiple alignments and build sequence divergence trees.

58 ultaneously informed by genetic diversity in multiple alignments and experimental design constraints

59 Pfam contains multiple alignments and hidden Markov model based profil

60 the underlying genomic features that lead to multiple alignments and investigate how they generate sy

61 g microbial communities are usually based on multiple alignments and phylogenetic inference, making t

62 , rapid, and accurate method, independent of multiple alignments and phylogenetic inference, to suppo

63 Gene predictions, multiple alignments and phylogenetic trees are freely av

64 Subsequently, multiple alignments and phylogenetic trees were calculat

65 Pfam is a collection of multiple alignments and profile hidden Markov models of

66 r provides access to the alignment analysis, multiple alignment, and comparative modeling tools.

67 ence evolution models for each position of a multiple alignment, and extending this idea to a joint e

68 hniques were used to locate motifs, generate multiple alignments, and assign PEP or OEP function to h

69 e subfamily sample size is too small for the multiple alignment approach.

70 d of the new algorithm was comparable to the multiple alignment approach.

71 idated via comparison to popular progressive multiple alignment approaches, ClustalW and T-Coffee, an

72 For this measure, columns in a multiple alignment are treated as character frequency ve

73 While evolutionary profiles in the form of a multiple alignment are used to derive these simple 'stru

74 Our whole-genome multiple alignments are available through the VISTA Brow

75 y, DNA and corresponding amino acid sequence multiple alignments are available together with high qua

76 The multiple alignments are constructed for protein structur

77 The SISYPHUS multiple alignments are displayed with SPICE, a browser

78 Multiple alignments are guided by a dendrogram computed

79 Multiple alignments are treated as sequences of amino ac

80 profile diversity, one should include in the multiple alignment as many confident sequence homologs a

81 The paper evaluates the multiple-alignment aspect of the SAM-T99 protocol, using

82 ur use of MULTIZ to produce the whole-genome multiple alignments at the Santa Cruz Genome Browser.

83 lutionary information, expressed in terms of multiple alignments, both at the input and output levels

84 based on the popular progressive approach to multiple alignment but avoids the most serious pitfalls

85 ylo-VISTA, an interactive tool for analyzing multiple alignments by visualizing a similarity measure

86 Alternatively, an existing multiple alignment can be processed.

87 oximations for assessing the significance of multiple alignments can be be very inaccurate.

88 Multiple alignments can be viewed or downloaded in six d

89 added to the observed amino acid counts in a multiple alignment column.

90 he proposed algorithm has successfully built multiple alignments comparable to other programs with si

91 Local multiple alignments computed by Mulan ensure reliable re

92 ificant new annotations include a 60-species multiple alignment conservation track on the mouse, upda

93 WAG+gamma+/-F, made on a test dataset of 380 multiple alignments containing protein sequences from al

94 ss including uploading sequences, creating a multiple alignment, deriving CODEHOPs and calculating th

95 detail by embedding the query sequence into multiple alignment displays and by mapping onto three-di

96 identify recombinant sequences within a DNA multiple alignment (either automatically or via manual i

97 STAMP also automatically builds multiple alignments, familial binding profiles and simil

98 ltiple DNA sequence alignments into a single multiple alignment file.

99 e present an Eulerian path approach to local multiple alignment for DNA sequences.

100 and then extracts the blastn query-anchored multiple alignment for this sequence.

101 proximately 72 000 motif sequences and >1300 multiple alignments for all PROSITE patterns, including

102 or maximizes the posterior distribution over multiple alignments for any number of DNA or protein seq

103 Interactive examination of RNA multiple alignments for covariant mutations is a useful

104 Multiple alignments for each homology group are stored a

105 nal Blocks Database, which contains ungapped multiple alignments for families documented in Prosite,

106 ows biomedical researchers to quickly obtain multiple alignments for genomic sequences and to subsequ

107 The database of multiple alignments for protein structures (DMAPS) provi

108 query system has been developed to retrieve multiple alignments for these families using the PDB cha

109 The server can be used to get multiple alignments for up to 25 protein structural chai

110 resence of a barcode gap (using pairwise and multiple alignments), formation of monophyletic groups u

111 The multiple alignment-free statistics are more sensitive to

112 Obtaining a multiple alignment from a set of sequences is quite a ch

113 PicXAA greedily builds up the multiple alignment from sequence regions with high local

114 in distinguishing high and moderate quality multiple alignments from low quality ones, with supporti

115 By applying phyloP to mammalian multiple alignments from the ENCODE project, we shed lig

116 neighbor approach (BLAST), methods based on multiple alignments generated by a statistical profile H

117 revised tree building procedure based on the multiple alignments generated during the process and (vi

118 Examination of the pairwise and multiple alignments in a region allows one to draw infer

119 In order to solve the task of computing multiple alignments in affordable time, the most commonl

120 for inferring the evolutionary history of a multiple alignment, in terms of both substitutions and,

121 We present an algorithm for multiple alignments, in which several PPI networks are a

122 Our extensions use multiple alignment information to define the boundaries

123 Multiple Alignment is a new interface for performing and

124 The multiple alignment is used to build a phylogenetic tree

125 Nevertheless, the computation of optimal multiple alignments is important in its own right, and i

126 imination using barcode gap analysis (with a multiple alignment) is 81.6% within 10x10 km squares and

127 Thus, in a traditional multiple alignment it is often difficult to directly vis

128 family; and (vi) the new Local Alignment of Multiple Alignments (LAMA) method to search a block agai

129 tion at a logo position as a per-observation multiple alignment log-odds score.

130 dividual transcription factor binding sites, multiple alignments markedly increase the signal-to-nois

131 ccount for dipolar coupling data measured in multiple alignment media is investigated using an intuit

132 We developed PROMALS, a multiple alignment method that shows promising results f

133 s in affordable time, the most commonly used multiple alignment methods have to use heuristics.

134 he major difference between ABA and existing multiple alignment methods is that ABA represents an ali

135 Of the multiple alignment methods tested, ours performed the be

136 ts into a protein sequence by constructing a multiple alignment model of the family.

137 n hidden Markov model (HMM) transducer-based multiple alignment model, and can analyze sequence data

138 ction strategy is presented that generates a multiple alignment more similar to those refined by huma

139 puter methods for iterative database search, multiple alignment, motif analysis and structural modeli

140 For maximum unification, the multiple alignments must reach into the twilight zone of

141 protein motifs) as well as manually adjusted multiple alignments obtained from ClustalW.

142 Analysis of an HMM-generated multiple alignment of 130 LAGLIDADG family members and t

143 Using a multiple alignment of 175 cytochrome P450 (CYP) family 2

144 t any two positions within a PWM, based on a multiple alignment of 5 mammalian genomes.

145 A multiple alignment of a large collection of these sequen

146 minutes on a personal computer to obtain the multiple alignment of all 12 sequences.

147 specific change in evolutionary rate using a multiple alignment of amino acid sequences for a given p

148 In this paper, a multiple alignment of amino acid sequences was construct

149 s also the fastest program evaluated for the multiple alignment of assembled human chromosome sequenc

150 e ABA (A-Bruijn alignment), a new method for multiple alignment of biological sequences.

151 Multiple alignment of deduced amino-acid sequences of gl

152 Multiple alignment of FGD and MER proteins revealed four

153 Multiple alignment of FGD with the hypothetical proteins

154 We illustrate our method by applying it to a multiple alignment of four HIV2 sequences, as well as of

155 superfamilies and sequence identifiers; and multiple alignment of genomic, PDB and custom sequences.

156 database search into the form of a coloured multiple alignment of hits stacked against the query.

157 ethods for detecting coevolving sites from a multiple alignment of homologous nucleotide or amino aci

158 on derived from the template structure and a multiple alignment of its homologs.

159 Multiple alignment of KAS amino acid sequences indicated

160 , we present a WWW-based software system for multiple alignment of large genomic sequences.

161 Using a multiple alignment of more than a megabase of contiguous

162 A new symmetric-iterative method for multiple alignment of protein sequences is presented.

163 We consider the problem of multiple alignment of protein sequences with the goal of

164 tool that implements a general framework for multiple alignment of protein sequences.

165 election at single amino acid sites, using a multiple alignment of protein-coding sequences for a giv

166 ng approaches for phylogenetic inference use multiple alignment of sequences and assume some sort of

167 First, an accurate multiple alignment of sequences of all members of a prot

168 The designed sequences provide a multiple alignment of sequences that all adopt the same

169 Multiple alignment of the 16 newly sequenced KSHV genome

170 A multiple alignment of the 32 complete genome sequences w

171 nment of all the available HIV genomes and a multiple alignment of the entire human, mouse, and rat g

172 logy model in Protein Data Bank format and a multiple alignment of the FVIII amino-acid sequencies fr

173 inst the non-redundant SwissProt to obtain a multiple alignment of the input sequence.

174 A multiple alignment of the sequences suggests a modular s

175 We have built a whole-genome multiple alignment of the three currently available mamm

176 A multiple alignment of these sequences revealed seven con

177 Regulatory motifs can be found by local multiple alignment of upstream regions from coregulated

178 Most algorithms for multiple alignment of whole genomes rely either on a ref

179 re, we use phylogenetic profiling to analyze multiple alignments of 24 human duplicon families that s

180 More divergent regions of multiple alignments of 3'UTRs are often more G- and/or C

181 The Blocks Database contains multiple alignments of conserved regions in protein fami

182 The Blocks Database contains multiple alignments of conserved regions in protein fami

183 ores and a comprehensive library of explicit multiple alignments of distantly related protein familie

184 for detecting interspecies recombination in multiple alignments of DNA sequences.

185 We created a comprehensive database of multiple alignments of each type of cadherin domain.

186 Multiple alignments of ERV1/ALR proteins indicated an in

187 t extends the use of these tools to imported multiple alignments of families not present in the datab

188 nts in vertebrate genomes, using genome-wide multiple alignments of five vertebrate species (human, m

189 Parallel searches have been performed with multiple alignments of four insect species (three specie

190 Prior and new multiple alignments of fungal antizyme mRNA sequences fr

191 h sequences of known structure, and includes multiple alignments of genome and PDB sequences.

192 Multiple alignments of genome sequences are helpful guid

193 software tool that processes and manipulates multiple alignments of genomic sequence.

194 nomics, based on algorithms for pairwise and multiple alignments of genomic sequences and whole-genom

195 When studying multiple alignments of genomic sequences one frequently

196 One of its main uses is to produce multiple alignments of homologs of the target sequence.

197 ositioning data, we show that the pattern in multiple alignments of internal exon and intron sequence

198 i-LAGAN is a practical method for generating multiple alignments of long genomic sequences at any evo

199 or carrying out likelihood-based analyses on multiple alignments of molecular sequence data, with the

200 In parallel, multiple alignments of naturally occurring sequences can

201 developed Partition-Assisted Clustering and Multiple Alignments of Networks (PAC-MAN) for the fast a

202 te ones and access ATGC-derived data such as multiple alignments of orthologous proteins, matrices of

203 Multiple alignments of prerecombination and postrecombin

204 ular, this results in a database of explicit multiple alignments of protein families in the twilight

205 ding, for example, to a database of explicit multiple alignments of protein families in the twilight

206 Protein profiles may be abstracted from multiple alignments of protein sequences, and substituti

207 Multiple alignments of proteins are an effective way of

208 omain structure, and allows one to construct multiple alignments of proteins containing (1) domains t

209 Multiple alignments of putative cellulose synthases from

210 into a probabilistic model which can analyze multiple alignments of reads.

211 P2 program produces an ordered list of local multiple alignments of similar regions among sequences,

212 eric, computes and displays nucleotide-level multiple alignments of the same sequences, together with

213 Multiple alignments of the sequences corresponding to th

214 and displays 1 Kb views of nucleotide-level multiple alignments of the sequences, together with anno

215 Through multiple-alignment of transposase sequences from a diver

216 n, search criteria creation, sequence and 3D multiple alignment options.

217 dict CRMs from known motifs either depend on multiple alignments or can only deal with a small number

218 c when binding sites are not well aligned in multiple alignments or when the number of input known mo

219 The final multiple alignment outperforms most state-of-the-art MST

220 or large datasets (bigBed and bigWig), a new multiple alignment output tool, links to variation and p

221 x stages in the form-and-polish strategy for multiple alignment: parameter choice, distance estimatio

222 wed that the algorithm consistently improves multiple alignment performance.

223 The constant check by the multiple alignment phase allows the search phase to be p

224 uence, proceeding to homolog identification, multiple alignment, phylogenetic tree construction, subf

225 o explore more detailed information, such as multiple alignments, phylogenetic trees and genomic neig

226 These multiple alignments pose substantial challenges to exist

227 conserved blocks within previously computed multiple alignments, primarily for DNA sequences.

228 e algorithm for rigorously solving the local multiple alignment problem.

229 tected between reads and then corrected by a multiple-alignment process; (ii) corrected reads are ass

230 New enhancements include a multiple alignment processor that extends the use of the

231 HOP designer is linked to BlockMaker and the Multiple Alignment Processor within the Blocks Database

232 Such sets can be used for multiple alignments, profile hidden Markov models and ot

233 equence segments for alignment in a standard multiple alignment program (MULTAL).

234 mbled into distinct species groups using the multiple alignment program CAP2 and are annotated with i

235 We describe a multiple alignment program named MAP2 based on a general

236 a (SIMD) technology was implemented into the multiple alignment program Praline by using 'message pas

237 MAVID is a multiple alignment program suitable for many large genom

238 nd non-coding regions and the Gibbs sampling multiple alignment program.

239 We describe a new global multiple-alignment program capable of aligning a large n

240 In addition, multiple alignment programs generally cannot deal with t

241 tion of the performance of MAP2 and existing multiple alignment programs.

242 Multiple alignments provided a method to estimate the nu

243 In this paper we report on tests of multiple alignment quality, comparing SAM-T99 to the sta

244 ured by an objective function which measures multiple alignment quality.

245 SMAL is especially useful when multiple alignments relative to a particular PPIN are re

246 imple formulas and pattern specifications to multiple alignments, reporting the positions and counts

247 domains for a non-redundant data set of 414 multiple alignments, representing 185 single and 231 mul

248 Comparison of domain architectures and multiple alignments resulted in the delineation of synap

249 However, phylogenetic analysis based on multiple alignments revealed that LSP-1 calliphorin and

250 Multiple alignment reveals group-specific domains outsid

251 nt framework, and predicting structures from multiple alignment samples instead of a single fixed ali

252 The multiple alignment showed some conserved columns, and th

253 arch has been made to improve the quality of multiple alignments, since misaligned parts of the multi

254 erage of the genome and without the need for multiple alignment steps, extensive homology searches, o

255 thods (local or global, gapped or ungapped), multiple alignment strategies and tree-building methods.

256 The multiple alignment strategy does not work for all types

257 The codon-equivalent multiple alignment suite begins conservational analysis

258 The prediction is based on a multiple alignment that contains both reference sequence

259 respective characteristics, and through the multiple alignment that describes their global relations

260 We introduce a novel approach to multiple alignment that is based on an algorithm for rap

261 It then constructs a multiple alignment that is maximally consistent with the

262 In particular, there is no score for multiple alignment that is well founded and treated as a

263 These genomes can be combined in a multiple alignment that provides useful information abou

264 Next, we showed by multiple alignment that the region of GCS flanking His-1

265 The server allows a single sequence or multiple alignment to be submitted, and returns predicti

266 ithm that uses the information implicit in a multiple alignment to dynamically build an index that is

267 nown phylogenetic tree on the species in the multiple alignment to improve the quality of its compute

268 use-chicken (HMC) and human-mouse-frog (HMF) multiple alignments to compile conserved blocks of synte

269 provides three services: sequence searching, multiple alignments to sequences of known structure, and

270 eleven mouse members were first analyzed in multiple alignments to visualize both reported and unrep

271 We present a new multiple alignment tool for whole genomes named Mugsy.

272 Opal, a multiple alignment tool that implements the best methods

273 ace, a built-in BLAST result parser, several multiple alignment tools, clustering algorithms and vari

274 provement in alignment accuracy over MUSCLE, Multiple Alignment using Fast Fourier Transform (MAFFT),

275 lgorithm, iterative global optimization of a multiple alignment using the MC algorithm and formatting

276 lude RNA secondary structure prediction from multiple alignments using either a thermodynamic approac

277 e equivalences that are then integrated into multiple alignments using sequence alignment tools.

278 ese were compared to profiles generated from multiple alignments using the consensus approach.

279 Multiple Alignment Variation Linker (MAVL) and StickWRLD

280 MAVL (multiple alignment variation linker) and StickWRLD provi

281 Herein, we present MAVL (Multiple Alignment Variation Linker) and StickWRLD.

282 mes, and for each genome a template-anchored multiple alignment was constructed.

283 ork, in which the matrix A now describes the multiple alignment, we adapted the QR factorization to p

284 his evaluation, given a gold standard set of multiple alignments, we calculate the probability that a

285 functional and structural studies of 14-3-3, multiple alignments were constructed from forty-six 14-3

286 hms produces optimal, gapped alignments, and multiple alignments when a region of the query sequence

287 We introduce a novel approach to RNA multiple alignment which couples a generative probabilis

288 s with its databases of domain sequences and multiple alignments whilst concurrently identifying comp

289 for the first time a general formulation for multiple alignment with arbitrary gap-costs based on an

290 Moreover, comparison of multiple alignment with motif analysis shows that the tw

291 Multiple alignments with consensuses are determined for

292 eloped an automated procedure which combines multiple alignments with structure prediction algorithms

293 le alignments, since misaligned parts of the multiple alignment yield misleading predictions.