ライフサイエンスコーパス: sequence alignment

1 y sequences and database hits using pairwise sequence alignment.

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

3 complexity hinders its accurate assembly via sequence alignment.

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

5 BLAST and avoids the complexity of multiple sequence alignment.

6 , tree construction, split decomposition and sequence alignment.

7 edictions can benefit homology modelling and sequence alignment.

8 sponded to Gly-284 of ArsC in the amino acid sequence alignment.

9 ide-by-side and navigated by a corresponding sequence alignment.

10 tool for membrane proteins based on multiple sequence alignment.

11 an be useful for downstream analysis such as sequence alignment.

12 more uniform amplification and more accurate sequence alignment.

13 ncluding for example an interactive multiple sequence alignment.

14 a different interpretation than conventional sequence alignment.

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

16 SFESA web server to refine pairwise protein sequence alignments.

17 served sites, and rely heavily upon multiple sequence alignments.

18 mputation of 3D structure based multiple RNA sequence alignments.

19 TurboFold by additionally providing multiple sequence alignments.

20 ses and to create potentially large multiple sequence alignments.

21 ent with a phylogeny derived from amino acid sequence alignments.

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

23 ikelihood methods from good quality multiple sequence alignments.

24 nclusion could not have been determined from sequence alignments.

25 n recent years as an alternative to multiple sequence alignments.

26 on correlated mutations detected in multiple sequence alignments.

27 ase pairing induces pairwise covariations in sequence alignments.

28 timate site-specific substitution rates from sequence alignments.

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

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

31 orough quality control procedure on multiple sequence alignments, aiming to provide minimum false-pos

32 BLAST is a heuristic biological sequence alignment algorithm which has been used by bioi

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

34 Sequence alignment algorithms are a key component of man

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

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

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

38 have motivated a search for high-efficiency sequence alignment algorithms.

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

40 rming the IC pockets, together with multiple sequence alignments, allowed us to propose a functional

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

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

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

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

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

46 We also engineered mutations based on sequence alignment and conserved amino acids in selected

47 Sequence alignment and domain analysis revealed the pres

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

49 Based on sequence alignment and further biochemical analysis, the

50 The amino acid sequence alignment and GEF activity studies also uncover

51 Sequence alignment and homology modeling showed that the

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

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

54 Sequence alignment and phylogenetic tree indicated that

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

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

57 nt (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g.

58 According to sequence alignment and protein structure predictions, th

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

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

61 Here, sequence alignment and structural modeling indicated tha

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

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

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

65 Sequence alignment and variant calling were performed fo

66 Sequence alignment and variant filtering detected HLH ge

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

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

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

70 Derived sequence alignments and chemical probing data from prote

71 Using sequence alignments and computational approaches, we her

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

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

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

75 Using sequence alignments and homology modeling, we designed a

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

77 The construction of multiple sequence alignments and inference of huge phylogenies co

78 revious versions, eggNOGv4 provides multiple sequence alignments and maximum-likelihood trees, as wel

79 Sequence alignments and phylogenetic analysis show that

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

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

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

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

84 nified framework for creating logos for both sequence alignments and profile hidden Markov models.

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

86 are captured in phylogenetic trees, multiple sequence alignments and statistical models (hidden Marko

87 Sequence alignments and the locations of highly conserve

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

89 The tmRNA Website serves tmRNA sequences, alignments and feature annotations, and has r

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

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

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

93 searching by hidden Markov models, multiple sequence alignment, and phylogenetic tree inference with

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

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

96 ia and methods available to perform multiple sequence alignments, and among these, the minimization o

97 s can be produced in the absence of multiple sequence alignments, and we propose that these trees wil

98 sidues for protein structure prediction from sequence alignments; and distinguishing strong collabora

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

100 ficult to address by conventional homologous sequence alignment approaches.

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

102 Using a Can1-Lyp1 sequence alignment as a guideline and a three-dimensiona

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

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

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

106 rhesus chromosomes according to their probe sequence alignments as displayed in the human and rhesus

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

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

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

110 city up to 85%), as compared with a multiple sequence alignment-based method (sensitivity 57%, and sp

111 ssential residues is not always apparent via sequence alignments because these are limited by the dep

112 Amino acid sequence alignments between bVP24 and eVP24 also identif

113 Current sequence alignment browsers allow visualization of large

114 , this server allows for refinement of HIV-1 sequence alignment by using N-linked glycosylation sites

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

116 , most methods developed for protein and DNA sequence alignment can be directly applied.

117 improved using effective filtering based on sequence alignment characteristics.

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

119 ing reads, ortholog identification, multiple sequence alignment, concatenation, phylogenetic tree est

120 RNA families represented by manually curated sequence alignments, consensus secondary structures and

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

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

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

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

125 search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pair

126 eport a method based on analysis of multiple sequence alignments, embodied in our program Janus, for

127 Sequence alignments enabled classification of the evasin

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

129 Sequence alignments, evolutionary analysis, and signatur

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

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

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

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

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

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

136 Sequence alignments form the basis for many comparative

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

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

139 Multiple sequence alignments from the venom gland transcriptome s

140 inference of phylogenetic trees and multiple sequence alignments from unaligned molecular sequences.

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

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

143 s (CMs) from structurally annotated multiple sequence alignments given as input.

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

145 Multiple sequence alignments have been constructed across high qu

146 quence alignment in the progressive multiple sequence alignment heuristic.

147 ore, in contrast to the conventional, linear sequence alignment, homologies between sugar- and H(+)-b

148 Structure modeling and sequence alignments identified a unique set of amino aci

149 Structural and sequence alignments identified three conserved acidic re

150 Sequence alignments identify the CNS-expressed gene MBLA

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

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

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

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

155 Guide trees are used to decide the order of sequence alignment in the progressive multiple sequence

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

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

158 Phylogenetic analysis and sequence alignment indicate that Cdc13B probably arose t

159 uggests these are noncatalytic, and multiple-sequence alignments indicate that they are unique among

160 Interestingly, sequence alignments indicated that, similar to FXa, resi

161 Sequence alignment indicates a general applicability to

162 The sequence alignment is a fundamental problem in bioinform

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

164 Sequence alignment is a long standing problem in bioinfo

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

166 A multiple sequence alignment is obtained from these probabilities

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

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

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

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

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

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

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

174 e commonly used file formats, including BAM, sequence alignment map, Wiggle, BigWig, browser extensib

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

176 space fastq format and outputs alignments in Sequence Alignment/Map format.

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

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

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

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

181 For RNA sequence alignment, most methods developed for protein a

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

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

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

185 Multiple sequence alignment (MSA) is a prominent method for class

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

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

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

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

190 oteins that have large good-quality multiple sequence alignments (MSA) because the power of correlate

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

192 Multiple sequence alignments (MSAs) are a prerequisite for a wide

193 Multiple sequence alignments (MSAs) are usually scored under the

194 (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sourc

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

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

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

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

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

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

201 Sequence alignment of 39 DPP-IV inhibitory peptides havi

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

203 Sequence alignment of CpGAL with other known plant beta-

204 ss-link by electrophoresis, MS, and multiple sequence alignment of de novo transcriptome and availabl

205 Primary sequence alignment of different Cxs shows the presence o

206 domain identified in this study by multiple sequence alignment of DYX1C1 proteins recovered from a w

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

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

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

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

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

212 rative, annotated, structure-based, multiple-sequence alignment of R2 subunits, identified a clade of

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

214 tivity of GAS was investigated by amino acid sequence alignments of 1,10- and 1,11-synthases and comp

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

216 Multiple-sequence alignments of A19 homologs indicated conservati

217 Multiple sequence alignments of each orthologous intron group wer

218 Multiple sequence alignments of evolutionarily distant protozoan,

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

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

221 genome-based phylogeny, genome synteny, and sequence alignments of orthologous genes and intergenic

222 Sequence alignments of promoters in prokaryotes postulat

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

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

225 lly derive consensus sequences starting from sequence alignments of proteins from Flaviviruses (from

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

227 Sequence alignments of the crystallized fragment of PvRB

228 Sequence alignments of the esterase domains in BiFae1B w

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

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

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

232 They render the information contained in sequence alignments or profile hidden Markov models by d

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

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

235 Each family is represented by a multiple sequence alignment, predicted secondary structure and co

236 with a protein sequence it returns: multiple sequence alignments, predicted aspects of structure (sec

237 Sequence alignments previously identified certain conser

238 e developed a method that integrated profile-sequence alignment, profile-profile alignment, and Domai

239 Multiple sequence alignment programs tend to reach maximal accura

240 % more accurate than popular next-generation sequencing alignment programs when processing mate pair

241 e-consuming process for most next-generation sequencing alignment programs.

242 Sequence alignment quantifies neuronal similarity by ide

243 cross eubacterial phyla, we created multiple sequence alignments representing 10 of these messenger R

244 Sequence alignment revealed a consensus motif overlappin

245 Sequence alignment revealed that GPR139 is highly conser

246 Sequence alignments revealed conserved motifs and sugges

247 Sequence alignment reveals that the T. brucei enzyme is

248 Sequence alignment reveals two consensus regions, contai

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

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

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

252 Sequence alignments show that the lipid-interaction site

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

254 A multiple sequence alignment shows that these three crucial amino

255 This includes methods for multiple sequence alignment, substitution model selection, evolut

256 Sequence alignment suggests that TDP2 contains four cons

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

258 Additional information includes multiple sequence alignments, tab-separated files of functional a

259 tions for each modelled loop, and a multiple sequence alignment that incorporates the query and templ

260 complexa genes identified several unreliable sequence alignments that had escaped previous detection,

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

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

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

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

265 the comparative modeling process, including sequence alignment, threading and loop building.

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

267 are relatively slow because they use protein sequence alignment to build feature vectors for allergen

268 Using sequence alignment to infer cysteine dioxygenase activit

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

270 ge datasets of genome intervals (e.g. genes, sequence alignments) to place their experimental results

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

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

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

274 to improve the results from various multiple sequence alignment tools.

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

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

277 variant identification, including tools for sequence alignment, tumor-germline comparison, and molec

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

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

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

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

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

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

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

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

286 crystal structures and a comprehensive KARI-sequence alignment, we identified key cofactor specifici

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

288 dels of amino acid substitution and multiple sequence alignment which is an NP-hard problem and requi

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

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

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

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

293 Through sequence alignment with known GKAPs and secondary struct

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

295 ped a model for HIV-1 IN-based solely on its sequence alignment with PFV IN-that differs in several w

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

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

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

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

300 ased model of Nav1 channels derived from the sequence alignment without insertions/deletions, the out