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 l program that uses blastn to produce such a multiple alignment.

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

15 e standard progressive alignment approach to multiple alignment.

16 single matches are consistent with a partial multiple alignment.

17 nd then incorporates them into a progressive multiple alignment.

18 utilize explicitly evolutionary profiles and multiple alignments.

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

20 are systematically tracked in the context of multiple alignments.

21 We extend the BLAST theory to multiple alignments.

22 le success developing statistical scores for multiple alignments.

23 sing a partial order graph representation of multiple alignments.

24 served transcription factor binding sites in multiple alignments.

25 hat combines SwissProt annotations with Pfam multiple alignments.

26 merging sequences or parts of sequences into multiple alignments.

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

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

29 ed by the difficulty of obtaining reasonable multiple alignments.

30 airwise alignments can be extended to making multiple alignments.

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

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

33 alculated from the posterior distribution of multiple alignments.

34 nnealing approach for exploring the space of multiple alignments.

35 ting complete ancestral sequences from large multiple alignments.

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

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

38 define a posterior distribution of possible multiple alignments.

39 ites as a measure of gene-structure based on multiple alignments across vertebrates of homologs of AD

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

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

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

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

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

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

46 Multiple alignments among genomes are becoming increasin

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

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

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

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

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

52 Multiple alignment and phylogenetic analysis of the prot

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

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

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

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

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

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

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

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

61 Pfam contains multiple alignments and hidden Markov model based profil

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

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

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

65 Subsequently, multiple alignments and phylogenetic trees were calculat

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

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

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

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

70 ggests future directions for sonification of multiple alignments: animated visualisation indicating t

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

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

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

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

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

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

77 The multiple alignments are constructed for protein structur

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

79 Multiple alignments are guided by a dendrogram computed

80 Multiple alignments are treated as sequences of amino ac

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

82 d visualisation indicating the column in the multiple alignment as the sonification progresses, user

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

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

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

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

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

88 Alternatively, an existing multiple alignment can be processed.

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

90 Multiple alignments can be viewed or downloaded in six d

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

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

93 Local multiple alignments computed by Mulan ensure reliable re

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

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

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

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

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

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

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

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

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

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

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

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

106 Multiple alignments for each homology group are stored a

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

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

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

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

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

112 alignments are stored in formats such as the Multiple Alignment Format (MAF).

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

114 The multiple alignment-free statistics are more sensitive to

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

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

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

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

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

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

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

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

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

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

125 Our extensions use multiple alignment information to define the boundaries

126 Multiple Alignment is a new interface for performing and

127 The multiple alignment is used to build a phylogenetic tree

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

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

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

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

132 paralogous sequences-to distinguish between multiple alignment locations.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

149 A multiple alignment of a large collection of these sequen

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

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

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

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

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

155 Multiple alignment of deduced amino-acid sequences of gl

156 Multiple alignment of FGD and MER proteins revealed four

157 Multiple alignment of FGD with the hypothetical proteins

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

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

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

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

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

163 Multiple alignment of KAS amino acid sequences indicated

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

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

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

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

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

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

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

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

172 ch as deep learning classifiers that rely on multiple alignment of sequences of homologous proteins,

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

174 Multiple alignment of the 16 newly sequenced KSHV genome

175 A multiple alignment of the 32 complete genome sequences w

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

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

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

179 A multiple alignment of the sequences suggests a modular s

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

181 A multiple alignment of these sequences revealed seven con

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

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

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

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

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

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

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

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

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

191 Multiple alignments of ERV1/ALR proteins indicated an in

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

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

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

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

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

197 Multiple alignments of genome sequences are helpful guid

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

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

200 When studying multiple alignments of genomic sequences one frequently

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

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

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

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

205 In parallel, multiple alignments of naturally occurring sequences can

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

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

208 Multiple alignments of prerecombination and postrecombin

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

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

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

212 Multiple alignments of proteins are an effective way of

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

214 Multiple alignments of putative cellulose synthases from

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

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

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

218 Multiple alignments of the sequences corresponding to th

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

220 Through multiple-alignment of transposase sequences from a diver

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

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

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

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

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

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

227 wed that the algorithm consistently improves multiple alignment performance.

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

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

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

231 These multiple alignments pose substantial challenges to exist

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

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

234 hes (multi-MUMs) help to frame and solve the multiple alignment problem.

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

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

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

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

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

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

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

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

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

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

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

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

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

248 Multiple alignments provided a method to estimate the nu

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

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

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

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

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

254 However, producing multiple alignments required for their analysis lags beh

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

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

257 Multiple alignment reveals group-specific domains outsid

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

259 The multiple alignment showed some conserved columns, and th

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

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

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

263 The multiple alignment strategy does not work for all types

264 The codon-equivalent multiple alignment suite begins conservational analysis

265 BLS crowdsources a multiple alignment task of 1 million 16S ribosomal RNA s

266 it the only protocol that can be applied to multiple alignment tasks and allow a structural comparis

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

286 Multiple Alignment Variation Linker (MAVL) and StickWRLD

287 MAVL (multiple alignment variation linker) and StickWRLD provi

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

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

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

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

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

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

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

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

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

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

298 Multiple alignments with consensuses are determined for

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

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