ライフサイエンスコーパス: sequence alignment

1 a different interpretation than conventional sequence alignment.

2 ncluding for example an interactive multiple sequence alignment.

3 cantly better than the results secured using sequence alignment.

4 cal and global quality of the input multiple sequence alignment.

5 complexity hinders its accurate assembly via sequence alignment.

6 ion/deletion model used in standard pairwise sequence alignment.

7 reduces the need for computationally costly sequence alignment.

8 a matrix-like array of numbers or a multiple-sequence alignment.

9 onsensus secondary structure and the optimal sequence alignment.

10 analyses are based on pre-estimated multiple sequence alignment.

11 ccurate inference by homology is an accurate sequence alignment.

12 y sequences and database hits using pairwise sequence alignment.

13 more uniform amplification and more accurate sequence alignment.

14 TurboFold by additionally providing multiple sequence alignments.

15 erforms as well as methods based on multiple sequence alignments.

16 ase pairing induces pairwise covariations in sequence alignments.

17 timate site-specific substitution rates from sequence alignments.

18 ted to improve the quality of large multiple sequence alignments.

19 SFESA web server to refine pairwise protein sequence alignments.

20 t, predicted natively disordered regions and sequence alignments.

21 ations are readily identifiable from primary sequence alignments.

22 coding genes can be detected within multiple sequence alignments.

23 -residue contact prediction even for shallow sequence alignments.

24 Gs (Clusters of Orthologous Genes), multiple sequence alignments, a set of 'index' orthologs represen

25 ergence of functional lineages in a multiple sequence alignment-a model for how sector properties mig

26 e browsers with evidence tracks derived from sequence alignments, ab initio gene predictors, RNA-Seq

27 e contacts in a sequence from its homologous sequence alignment across different species.

28 amming matrix in the Needleman-Wunsch global sequence alignment algorithm, and reconstruct phylogenet

29 Sequence alignment algorithms are a key component of man

30 Most high-throughput sequence alignment algorithms do not use contextual info

31 It uses efficient sequence alignment algorithms to minimize search times,

32 Despite the relative success of modern-day sequence alignment algorithms, so-called alignment-free

33 eral software packages, primarily relying on sequence alignment algorithms.

34 the analogous residues in Class 1 enzymes by sequence alignment alone.

35 lar and alpha-helical membrane proteins from sequence alignments alone, we developed an approach to p

36 of sequences SARA-Coffee outputs a multiple sequence alignment along with a reliability index for ev

37 To overcome these challenges, we have used sequence alignments, an anaerobic purification method, i

38 Using crystal structures, we generate sequence alignment analyses revealing four major structu

39 Homology modelling and sequence alignment analysis further facilitate the ratio

40 were detected in these proteins by multiple sequence alignment analysis.

41 dynamics on parameters derived from multiple sequence alignments analyzed by using direct coupling an

42 ich each family is represented by a multiple sequence alignment and a profile hidden Markov model (HM

43 Sequence alignment and domain analysis revealed the pres

44 programming algorithm that accounts for both sequence alignment and epigenome similarity.

45 HTSlib for BAM access, BWA-MEM and BLAT for sequence alignment and Fermi for error correction and se

46 Based on sequence alignment and further biochemical analysis, the

47 Sequence alignment and homology modeling showed distant

48 Sequence alignment and homology modeling showed that the

49 In the current study, we used sequence alignment and homology modeling to identify fea

50 of Potts models from structure prediction to sequence alignment and homology search by developing wha

51 t implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not

52 Sequence alignment and molecular structure analysis of t

53 Sequence alignment and phylogenetic tree indicated that

54 or Genomics) for reinforcing key concepts in sequence alignment and phylogenetic tree reconstruction.

55 most practical approach to problems such as sequence alignment and phylogeny, more rigorous approach

56 According to sequence alignment and protein structure predictions, th

57 y collects homologues, infers their multiple sequence alignment and reconstructs a phylogenetic tree

58 Phylogenetic analysis, sequence alignment and site-directed mutagenesis reveale

59 To assess TurboFold II, its sequence alignment and structure predictions were compar

60 esults highlight the importance of improving sequence alignment and the use of appropriate substituti

61 a suite of tools for downloading data, multi-sequence alignment and tree building supports a variety

62 Sequence alignment and variant calling were performed fo

63 me, target-enriched and nanopore sequencing, sequence alignment and variant detection.

64 Sequence alignment and variant filtering detected HLH ge

65 hyltransferases have been identified through sequence alignment and/or genetic analysis; however, few

66 m designed for the fast, scalable display of sequence alignments and annotations landscaped against a

67 mensional structural information or multiple sequence alignments and can even predict small interacti

68 Derived sequence alignments and chemical probing data from prote

69 Using sequence alignments and computational approaches, we her

70 two active site residues predicted based on sequence alignments and crystal structures, to be key to

71 e recognition databases and protein multiple sequence alignments and discuss possible interpretations

72 y webpages are available, including multiple sequence alignments and HMM profiles for each VOG.

73 Using sequence alignments and homology modeling, we designed a

74 ocal, global, and semi-global pairwise intra-sequence alignments and improves the performance of prev

75 ne learning, including high-quality multiple sequence alignments and insulated training/validation sp

76 oves both its utility in generating multiple sequence alignments and its heuristic utility.

77 Sequence alignments and phylogenetic analysis show that

78 etween protein sequences, rely upon multiple sequence alignments and phylogenetic trees of large data

79 ein sequences can be analysed using multiple sequence alignments and phylogenetic trees.

80 evant genome sequences to construct complete sequence alignments and phylogenies.

81 alth of information associated with multiple sequence alignments and presents them in an intuitive ma

82 ats and provides an interface to analyses of sequence alignments and sets of contact predictions.

83 nd TEN across species, we performed multiple sequence alignments and statistical coupling analysis on

84 represented in phylogenetic trees, multiple sequence alignments and statistical models (hidden Marko

85 omparison of the three methods showed deeper sequence alignments and the integration of domain-based

86 Sequence alignments and the locations of highly conserve

87 all aligned PPI networks and (ii) using both sequence alignments and topological NMTF-predicted score

88 ent the genetic variation observed after DNA sequencing, alignment and variant calling of a sample co

89 n of orthologous genes or proteins, multiple sequence alignment, and choice of substitution models an

90 s in existing databases, performs a multiple sequence alignment, and design primers based on sequence

91 systems such as sequence similarity search, sequence alignment, and phylogenetic inference.

92 Jmol or JSmol, along with the corresponding sequence alignment, and the option to download the nucle

93 n constraints derived from antibody multiple-sequence alignments, and (ii) during backbone design, ma

94 correlations between sites in deep multiple sequence alignments, and these pairwise couplings have i

95 thin the hmmsearch pipeline as well as other sequence alignment applications.

96 ationship studies, receptor mutagenesis, and sequence alignment are integrated to better understand p

97 Genomic-scale sequence alignments are increasingly used to infer phylo

98 ndel component of the probability of a given sequence alignment as a product of either probabilities

99 n of biological phenomena rely on a multiple sequence alignment as input.

100 tablished applications for multiple circular sequence alignment as well as single and structured moti

101 This approach uses multiple-sequence alignments, atomic-resolution structural inform

102 to produce results as effective as multiple-sequence alignment based methods for reconstruction of p

103 Using sequence alignment based on BCE minimal motif, the speci

104 gnment tool that can refine a given multiple sequence alignment based on suboptimal alignments genera

105 d 90%, as an alternative to conventional DNA sequence alignment-based approaches to identify putative

106 tivity and specificity for read-binning than sequence alignment-based methods, also executing in less

107 Amino acid sequence alignments between bVP24 and eVP24 also identif

108 Current sequence alignment browsers allow visualization of large

109 ical prediction of pairwise covariation from sequence alignments, but it initially showed limited uti

110 Skylign can avoid sampling bias in sequence alignments by down-weighting redundant sequence

111 BLAST creates local sequence alignments by first building a database of smal

112 The framework enables generation of sequence alignments, calculation and evaluation of evolu

113 improved using effective filtering based on sequence alignment characteristics.

114 These analyses include: a wide variety of sequence alignments, comparative analyses of multiple ge

115 inferring covariation signals from multiple sequence alignments, considers a broad range of other se

116 t could not be assigned by antibody germline sequence alignment could be correctly determined using t

117 fects of different read parameters on genome sequence alignment, coverage of different classes of gen

118 d analysis JavaScript component for Multiple Sequence Alignment data of any size.

119 Sequence alignments enabled classification of the evasin

120 Genome assembly, repeat detection, multiple sequence alignment, error detection and many other relat

121 cers across distantly related species, where sequence alignment fails, and the model highlights speci

122 rts the visualization of quality metrics for sequence alignment files for multiple experiments genera

123 The input to RAPIDR is a set of sequence alignment files in the BAM format, and the outp

124 d library for working with SAM, BAM and CRAM sequence alignment files; the most common file formats f

125 is compatible with all mappers that perform sequence alignment for verification.

126 We have collected manually curated sequence alignments for >3000 sequences, in vivo phenoty

127 coveries in selected viruses, we now analyze sequence alignments for approximately 700 RNA virus spec

128 f Fungi-Pezizomycotina (Ascomycota)-based on sequence alignments for six loci (nr5.8S, nrLSU, nrSSU,

129 ess to curated, representative ribosomal RNA sequence alignments from bacterial, archaeal, eukaryal a

130 gies for SNP and INDEL discovery incorporate sequence alignments from multiple individuals to maximiz

131 Multiple sequence alignments from the venom gland transcriptome s

132 e latter can be calculated from the multiple sequence alignments generated by PSI-BLAST.

133 We benchmarked MTMG on 1,033 sequence alignments generated for CASP9, CASP10 and CASP

134 dels for scoring insertions and deletions in sequence alignments has been hindered by algorithmic com

135 Multiple sequence alignments have been constructed across high qu

136 A kinome-wide sequence alignment highlighted a poorly conserved cystei

137 Structural and sequence alignments identified three conserved acidic re

138 Sequence alignments identify the CNS-expressed gene MBLA

139 Though various fast Smith-Waterman local sequence alignment implementations have been developed f

140 wed that structural alignment is better than sequence alignment in identifying good templates, suitab

141 to improve the accuracy of multiple circular sequence alignment in terms of the inferred likelihood-b

142 The user can submit a sequence alignment in the FASTA format and the correspon

143 s utilities for manipulating high-throughput sequence alignments in the Sequence Alignment/Map format

144 Sequence alignments including >110 000 HIV-1 partial pol

145 idely used methods for inferring homology by sequence alignment, including BLAST and profile hidden M

146 Multiple sequence alignment indicated that these trGTPases cluste

147 Sequence alignment inferred that the core structure of f

148 probe binding specificity from genome-scale sequence alignment information.

149 NeuSomatic summarizes sequence alignments into small matrices and incorporates

150 Here, we generated 2871 gene-family protein sequence alignments involving 9990 genes and performed m

151 Sequence alignment is a central operation in bioinformat

152 The sequence alignment is a fundamental problem in bioinform

153 ologous template proteins and their pairwise sequence alignment is a key step in protein comparative

154 Sequence alignment is a long standing problem in bioinfo

155 Protein sequence alignment is essential for a variety of tasks s

156 mal path to decide whether or not performing sequence alignment is necessary.

157 A multiple sequence alignment is obtained from these probabilities

158 her ultra-fast metagenomic classifiers, full sequence alignment is performed allowing for gene identi

159 ow however, the quality of the corresponding sequence alignment is usually poor, leading to poor perf

160 However, accurate large-scale multiple sequence alignment is very difficult, especially when th

161 Evolutionary information encoded in multiple sequence alignments is known to greatly improve sequence

162 ribe couplings between columns in a multiple sequence alignment it is possible to significantly incre

163 luding analyses at the whole genome multiple sequence alignment level.

164 e have the functionality to convert files in sequence alignment map or BigWig format.

165 g high-throughput sequence alignments in the Sequence Alignment/Map format.

166 onserved RNA structure, as opposed to when a sequence alignment merely has insufficient variation to

167 We present UPP, a multiple sequence alignment method that uses a new machine learni

168 fast clustering methods and slower multiple sequence alignment methods and provides a seamless trans

169 ing in biological sequences, the traditional sequence alignment methods become unsuitable and infeasi

170 tures: 1) instead of using multiple/pairwise sequence alignment methods, BSPAT adopts an efficient an

171 f bioinformatics is to use a single multiple sequence alignment (MSA) as the basis for various types

172 nt pipeline available for sensitive multiple sequence alignment (MSA) collection.

173 SSMs are built from the query-based multiple sequence alignment (MSA) implied by the pairwise alignme

174 While multiple sequence alignment (MSA) is a potent tool to detect the

175 ent a parsimonious, structure-based multiple sequence alignment (MSA) of 497 human protein kinase dom

176 ce profiles, which are derived from multiple sequence alignment (MSA) of sequence homologs in a prote

177 te Carlo (MCMC) sampler for protein multiple sequence alignment (MSA) that, as implemented in the pro

178 tors [i.e. deep learning technique, multiple sequence alignment (MSA), distance distribution predicti

179 in due to the requirement for large multiple sequence alignments (MSA) and the fact that, in general,

180 protein structure and function from Multiple Sequence Alignments (MSA) are emerging as powerful tools

181 ly used method for visualization of multiple sequence alignments (MSAs) and sequence motifs.

182 Multiple Sequence Alignments (MSAs) are a fundamental operation i

183 (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sourc

184 Reconstruction of multiple sequence alignments (MSAs) is a crucial step in most hom

185 nal and systematic information from multiple sequence alignments (MSAs) is becoming increasingly impo

186 nce matrix (or precision matrix) of multiple sequence alignments (MSAs) through deep residual convolu

187 , Uniclust30 and three databases of multiple sequence alignments (MSAs), Uniboost10, Uniboost20 and U

188 As) and some typical types of local multiple sequence alignments (MSAs), we numerically computed the

189 Highly divergent sites in multiple sequence alignments (MSAs), which can stem from erroneou

190 relationships between residues from multiple sequence alignments (MSAs).

191 ific choice of homologs included in multiple sequence alignments (MSAs).

192 ds rely on the availability of deep multiple sequence alignments (MSAs).

193 is (DCA) of correlated mutations in multiple sequence alignments (MSAs).

194 obtained from OrthoDB and randomly generated sequence alignments (non-homologs), successfully determi

195 Based on sequence alignment, NSP1-1 proteins from species B, G, a

196 ing consensus topology generated by multiple sequence alignment of a group of neurons reveals their s

197 The package only requires the multiple sequence alignment of a protein for inferring the co-evo

198 Primary sequence alignment of different Cxs shows the presence o

199 bstrate-docked structures that, coupled with sequence alignment of FraB homologs, helped map a putati

200 extract amino acid contacts from a multiple sequence alignment of homologues of the curli subunit pr

201 We generated an extensive sequence alignment of ionotropic glutamate receptors (iG

202 Through amino acid-sequence alignment of NADP(+)- and NAD(+)-preferred 6PGD

203 Global pairwise and multiple sequence alignment of neurite topologies enables detaile

204 A primary sequence alignment of PNT1 with clostripain and PmC11 re

205 profile is then constructed from a multiple sequence alignment of the interface analogies, which is

206 mmetry properties, the symmetry axis and the sequence alignment of the structures before and after th

207 utations of the TaRca2-beta isoform based on sequence alignment of the thermostable TaRca1-beta from

208 an identity of 51% based on multiple protein sequence alignments of 52 MdmX homologs.

209 Multiple sequence alignments of all structurally characterized pr

210 Multiple sequence alignments of each orthologous intron group wer

211 rkov models (HMMs), which represent multiple sequence alignments of homologous proteins.

212 okaryotic complexes for which large multiple sequence alignments of homologous sequences can be compi

213 s from various sources and generate multiple sequence alignments of identified clusters.

214 inference of phylogenetic networks from the sequence alignments of multiple, unlinked loci.

215 Sequence alignments of promoters in prokaryotes postulat

216 Using multiple sequence alignments of protein domains in the human geno

217 coevolution profiles extracted from multiple sequence alignments of protein families with their infer

218 features that can be extracted from multiple sequence alignments of putative homologous genes (orthol

219 Sequence alignments of the crystallized fragment of PvRB

220 Sequence alignments of the esterase domains in BiFae1B w

221 s concatenating several alternative multiple sequence alignments of the same sequences, produced usin

222 generation of reference-free Cactus multiple sequence alignments of these genomes, and the developmen

223 the long-anticipated possibility of putting sequence alignment on the same footing as statistical ph

224 irus epidemiological data, and viral protein sequence alignments on one page, and provides further in

225 ndly interface to BAM/SAM/CRAM files, global sequence alignment operations and sequence assembly.

226 Using the crystal structure, primary sequence alignment, pH-activity profiles, and site-direc

227 ences, particularly for splicing prediction, sequence alignment, phylogenetic analysis, and structure

228 were computed together with their associated sequence alignments, phylogenies, HMM models and functio

229 domain that was previously unrecognized from sequence alignments, placing cPLA2delta into the class o

230 d customize statistical images and search by sequence alignment, position or gene name.

231 Combining sequence alignment, probability analysis, and binding fr

232 Multiple sequence alignment programs tend to reach maximal accura

233 % more accurate than popular next-generation sequencing alignment programs when processing mate pair

234 Sequence alignment quantifies neuronal similarity by ide

235 3% of libraries were dropped because of low sequence alignment rates.

236 Sequence alignments reveal that Gram-positive NanK enzym

237 Furthermore, sequence alignments reveal this topological instability

238 Sequence alignment revealed that GPR139 is highly conser

239 Sequence alignment reveals two consensus regions, contai

240 Given a sequence alignment, RNAdetect can accurately detect the

241 GotCloud automates sequence alignment, sample-level quality control, varian

242 ork aligners and show that (i) by using only sequence alignment scores, Fuse already outperforms othe

243 The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web servi

244 Sequence alignments show that the lipid-interaction site

245 Multiple sequence alignment showed high conservation of amino aci

246 DNA sequence alignment showed that 19% or 62% of shotgun pyr

247 The consensus derived from the sequence alignment shows that the critical residues dete

248 Sequence alignment shows that these four residues involv

249 A multiple sequence alignment shows that these three crucial amino

250 methods for the curation of quality multiple sequence alignments since these public datasets represen

251 This presents an opportunity for DNA sequence alignment software to exploit high-concurrency

252 In this paper, we present ADEPT, a new sequence alignment strategy for GPU architectures that i

253 Sequence alignment suggests that the proposed catalytic

254 The viperin structure, together with sequence alignments, suggests that vertebrate viperins a

255 -read aligner, can compute WGS (whole-genome sequencing) alignments ten times faster than comparable

256 his enables the scalable generation of large sequence alignments that maintain high accuracy even on

257 sis (SCA) is a method for analyzing multiple sequence alignments that was used to identify groups of

258 he analysis of computer-simulated nucleotide sequence alignments that were evolved with non-stationar

259 ignments of query sequences against multiple sequence alignments; the redesign of the web pages and d

260 Despite the advances in recent decades on sequence alignment, threading and alignment-free methods

261 ation were (i) a core morph guided by a TLR7 sequence alignment to achieve a dual TLR7/8 antagonism p

262 and K900) in the VZV gBcyt was identified by sequence alignment to be conserved among alphaherpesviru

263 Using sequence alignment to compare more than 12,000 pairs of

264 Using sequence alignment to infer cysteine dioxygenase activit

265 identifying statistically significant local sequence alignments to evaluating matches to hidden Mark

266 been developed to utilize extensive protein sequence alignments to extract co-evolutionary signals o

267 Probs is a state-of-the-art protein multiple sequence alignment tool based on hidden Markov models.

268 ity and contact map visualizations, multiple sequence alignment tools for template-based modeling, ri

269 of biological sequences calls for speedup of sequence alignment tools such as BLAST.

270 c and clinical variations as well as protein sequence alignment tools.

271 T into popular third-party analysis tools or sequence alignment tools.

272 ucing gene and SNP annotation and generating sequence alignment tools.

273 io calculation of the probability of a given sequence alignment under a genuine stochastic evolutiona

274 As SneakySnake does not replace sequence alignment, users can still obtain all capabilit

275 on program JoY, formats a submitted multiple-sequence alignment using three-dimensional (3D) structur

276 od, COMPADRE (COmparison of Multiple Protein sequence Alignments using Database RElationships) assess

277 voted to developing pipelines for automating sequence alignment, variant calling, and annotation.

278 ly calculate the occurrence probabilities of sequence alignments via evolutionary processes on an ent

279 An interactive primers diagram, a sequence alignment viewer and a virtual electrophoresis

280 equence download options, and a new multiple sequence alignment viewer has been incorporated into the

281 Guided by sequence alignment, we created IDL deletions in human PK

282 Using structure-based sequence alignment, we were able to identify other putat

283 e, using bioinformatics analyses and protein sequence alignments, we found that in Arabidopsis thalia

284 Finally, by multiple sequence alignments, we observe that G-quadruplex-formin

285 Based on bioinformatic clustering and sequence alignments, we selected seven fungal AA9 LPMOs

286 On the basis of sequence alignments, we show that the structural feature

287 stence of an uncertainty induced by multiple sequence alignment when reconstructing phylogenies.

288 is task by automatically generating multiple sequence alignments (where appropriate) and finding stru

289 iled with the input sequence into a multiple sequence alignment which is mined for single-nucleotide

290 approaches to sequence analysis are based on sequence alignment, which is limited when dealing with l

291 or DECIPHER, a new context-aware program for sequence alignment, which outperformed other programs on

292 hylogenetic approaches are based on multiple sequence alignments, which analyze shared gene datasets

293 come widely available, structurally-informed sequence alignment will become broadly useful for de nov

294 able for substitutions can be identified via sequence alignment with a high degree of success.

295 Through sequence alignment with known GKAPs and secondary struct

296 n amino acid substitution that also restores sequence alignment with Old World monkeys, protected aga

297 VesB is likely produced as a zymogen because sequence alignment with trypsinogen identified a putativ

298 VG format with options to view full multiple sequence alignments with and without gaps and insertions

299 the repetitive element content, and produce sequence alignments with human and chimpanzee Y Chromoso

300 s based on the seed-and-extend approach from sequence alignment, with modifications specific to optic