ライフサイエンスコーパス: BLAST

1 BLAST analyses showed the closest homologs belonging to

2 BLAST analysis indicated that only two of the ORF protei

3 BLAST analysis of the A. niger genome for the presence o

4 BLAST analysis using EST sequences harboring SNPs with t

5 BLAST is a heuristic biological sequence alignment algor

6 BLAST is a routinely used tool for this purpose with ove

7 BLAST jobs that hitherto failed or slogged inefficiently

8 (BLAST presently does not permit its alignments to includ

9 BLAST provides sequence similarity searches of GenBank a

10 BLAST provides sequence similarity searches of GenBank a

11 BLAST provides sequence similarity searches of GenBank a

12 BLAST provides sequence similarity searches of GenBank a

13 BLAST provides sequence similarity searches of GenBank a

14 BLAST provides sequence similarity searches of GenBank a

15 BLAST provides sequence similarity searches of GenBank a

16 BLAST provides sequence similarity searches of GenBank a

17 BLAST provides sequence similarity searches of GenBank a

18 BLAST remains one of the most widely used tools in compu

19 BLAST searches and phylogenetic analyses indicate pXF-RI

20 BLAST searches indicated that the S. frugiperda rhabdovi

21 BLAST searches of the NCBInr protein database using the

22 BLAST searches with S. cerevisiae SR-like protein Npl3 (

23 BLAST-based characterizations of non-ribosomal RNA seque

24 BLAST-ing these novel contigs against all publically ava

25 s in the concordant contigs in two ways: (1) BLAST-ing each contig against normal RNA-Seq samples, (2

26 with 60,842 assembled transcripts and 30,518 BLAST hits.

27 A BLAST search of the Anabaena genome identified 166 hepA-

28 A BLAST search revealed that all three SNPs of interest (C

29 A BLAST search shows that the closest-related amidases alm

30 A BLAST utility was integrated and a phosphopeptide BLAST

31 or more of the three genes can be used as a BLAST query against the database which is Web accessible

32 In order to develop a BLAST-like tool for small molecules, one must first unde

33 profiles, nucleotide sequence information, a BLAST search tool and easy export of content via direct

34 ife, we tested their utility by performing a BLAST search against authenticate published ITS sequence

35 manipulated at the command-line to specify a BLAST candidate's query-coverage or percent identity req

36 s, which are subsequently classified using a BLAST comparison with a local version of KinBase, the cu

37 ible via organism pages, genome browsers and BLAST search engines, which are implemented via the open

38 omology search tools such as cross_match and BLAST variants, as well as Repbase, a collection of know

39 nnotations, comparable by gene families, and BLAST-searchable by user provided sequences.

40 Uniprot annotations, Gene Ontology (GO), and BLAST bioinformatics tools.

41 than that of baseline algorithms Gotcha and BLAST, which were based solely on sequence similarity in

42 ware/spocs.html; the Boost C++ libraries and BLAST are required.

43 ion of avian PB2 genes to other mammals, and BLAST sequence analysis identified a naturally occurring

44 Sequencing and BLAST search identified it as mannose-1-phosphate guanyl

45 y QPCR, agarose gel analysis, sequencing and BLAST, and all validation data can be freely accessed fr

46 nments based on 16S rRNA gene similarity and BLAST matches to predicted proteins.

47 local alignment programs HMMER, SSEARCH, and BLAST, and the popular ClustalW program with zero end-ga

48 expression, P-values), and both the text and BLAST searches.

49 n fact not an ideal tool for this purpose as BLAST is a local alignment algorithm and does not necess

50 tions where probabilistic algorithms such as BLAST might discourage attempts at greater certainty bec

51 eotide sequence database using tools such as BLAST to examine the potential targets.

52 tures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databas

53 escent theory and efficient software such as BLAST, ClustalW, Phylip, etc., provide the foundation fo

54 sequence similarity search services such as BLAST, FASTA, InterProScan and multiple sequence alignme

55 Tools such as BLAST, GBrowse and JBrowse for browsing genomes, express

56 ely the results of an alignment tool such as BLAST, limiting their estimation accuracy to high ranks

57 ed to sequence-level alignment tools such as BLAST.

58 speedup of sequence alignment tools such as BLAST.

59 At BLAST X we gained an appreciation for the lifestyle choi

60 re, we describe Leapfrog, a simple automated BLAST pipeline that leverages increased taxon sampling t

61 quence, structure and function via web-based BLAST searches.

62 analysis tools such as NCBI BLAST and Batch BLAST.

63 es orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an o

64 tools, most commonly based on bidirectional BLAST searches that are used to identify homologous gene

65 trez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, S

66 trez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Electronic PCR

67 MC), Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq

68 ral, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Sp

69 MC), Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Electro

70 tral (PMC), Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign,

71 Analysis by BLAST search revealed homologs to SdbA in other Gram-pos

72 Reads were annotated by BLAST (Basic Local Alignment Search Tool) search against

73 igs through contig-to-gene identification by BLAST nearest-neighbor comparison, and through single-co

74 restingly, an MCM homolog was identified, by BLAST analysis, within a phage integrated in the bacteri

75 sponded to the de novo-assembled sequence by BLAST analysis.

76 and their putative target insertion sites by BLAST searches followed by examination of the sequences

77 ctive evaluation of the use of point-of-care BLAST by ASPs.

78 of frameshift alignments, similar to classic BLAST statistics.

79 This tool combines BLAST with a global alignment algorithm to ensure a full

80 e alignment, phylogenetic tree construction, BLAST comparison and sequence variation determination ar

81 endent RNA polymerase missed by conventional BLAST searches, an emergent clade of tombus-like viruses

82 We have developed customizable BLAST tools that allow users to perform species- and exp

83 in three domains of life, with customizable BLAST tools.

84 A customized BLAST sequence similarity search is also developed for a

85 uding a Distributed Annotation Server (DAS), BLAST and a public MySQL database.

86 e-of-the-art tools, including HHblits, DELTA-BLAST and PSI-BLAST.

87 eration of programs in the popular PSI/DELTA-BLAST family of tools will not only speed-up homology se

88 methods based on sequence similarity (i.e., BLAST) have a dominant effect.

89 EC-BLAST has the potential to improve enzyme classification

90 We present EC-BLAST, an algorithm and Web tool for quantitative simila

91 nd place these on the phylogeny using either BLAST or phylogeny-based approaches, and then use the di

92 this question, we: (1) conducted exhaustive BLAST searches of MCR numts in three hominoid genomes; (

93 egration with remote services for on-the-fly BLAST and Primer BLAST analyses, graphical interfaces fo

94 ich include a graphical genome browser, FTP, BLAST search, a query optimised data warehouse, programm

95 Sequence-based search methods (e.g. BLAST) have been used to transfer such annotation inform

96 n Algorithm-Basic Local Alignment Tool (GDDA-BLAST), which derives structural, functional, and evolut

97 ial NCBI-BLAST, the speedups achieved by GPU-BLAST range mostly between 3 and 4.

98 processing unit (GPU), we have developed GPU-BLAST, an accelerated version of the popular NCBI-BLAST.

99 The source code of GPU-BLAST is freely available at http://archimedes.cheme.cmu

100 more, H-BLAST is 1.5-4 times faster than GPU-BLAST.

101 H-BLAST employs a locally decoupled seed-extension algorit

102 H-BLAST produces identical alignment results as NCBI-BLAST

103 We develop the heterogeneous BLAST (H-BLAST), a fast parallel search tool for a heterogeneous

104 Speedups achieved by H-BLAST over sequential NCBI-BLASTP (resp. NCBI-BLASTX) ra

105 Furthermore, H-BLAST is 1.5-4 times faster than GPU-BLAST.

106 o 10 (resp. With 2 CPU threads and 2 GPUs, H-BLAST can be faster than 16-threaded NCBI-BLASTX.

107 We develop the heterogeneous BLAST (H-BLAST), a fast parallel search tool for a heter

108 than the existing seeding strategies used in BLAST-like tools.

109 ng homology by sequence alignment, including BLAST and profile hidden Markov models (profile HMMs), a

110 small-cluster-based applications, including BLAST from the National Center for Biotechnology Informa

111 e of other commonly used programs, including BLAST, POY, MAFFT, MUSCLE and CLUSTAL.

112 rappers for key analysis programs, including BLAST, SignalP, TMHMM and InterProScan, and parsers for

113 for a wide range of result types, including BLAST and sequence motif queries.

114 muBLASTP, a novel database-indexed BLAST for protein sequence search, delivers identical hi

115 me level of sensitivity as the query-indexed BLAST, i.e., NCBI BLAST, or they can only support nucleo

116 ved from extensive computationally intensive BLAST comparisons of >2000 microbes.

117 with greater sensitivity than non-iterative BLAST.

118 decade has seen R and the Gene Ontology join BLAST and GenBank as the main components in bioinformati

119 lyses (VirulenceFinder, ResFinder, and local BLAST searches) were used to determine stx subtypes, mul

120 We assigned the OTUs by combining local BLAST searches with phylogenetic analyses.

121 Moreover, BLAST searches of the public synchronized databases with

122 uence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega

123 provides online analysis tools such as NCBI BLAST and Batch BLAST.

124 ivity as the query-indexed BLAST, i.e., NCBI BLAST, or they can only support nucleotide sequence sear

125 d end-to-end speedup over multithreaded NCBI BLAST.

126 engineered ZFPs, and direct querying of NCBI BLAST servers for identifying potential off-target sites

127 The NCBI BLAST URL is http://blast.ncbi.nlm.nih.gov.

128 end-to-end speedup over single-threaded NCBI BLAST.

129 ch, delivers identical hits returned to NCBI BLAST.

130 produces identical alignment results as NCBI-BLAST and its computational speed is much faster than th

131 entation is based on the source code of NCBI-BLAST, thus maintaining the same input and output interf

132 lerate BLASTX and BLASTP-basic tools of NCBI-BLAST.

133 ional speed is much faster than that of NCBI-BLAST.

134 , an accelerated version of the popular NCBI-BLAST.

135 In comparison to the sequential NCBI-BLAST, the speedups achieved by GPU-BLAST range mostly b

136 A new BLAST report allows faster loading of alignments, adds n

137 al significance, along with the advantage of BLAST/PSI-BLAST in terms of speed.

138 The widespread impact of BLAST is reflected in over 53,000 citations that this so

139 ster than miBLAST, another implementation of BLAST nucleotide searching with a preprocessed database,

140 d further to 81% (313/386) upon provision of BLAST (P < .001) without any increase in incidence of ad

141 gth of each gene requires multiple rounds of BLAST searches for a single IG sequence.

142 network (A2ApsN) that exploits the speed of BLAST and avoids the complexity of multiple sequence ali

143 Any improvement in the execution speed of BLAST would be of great importance in the practice of bi

144 tions completed the first and second step of BLAST architecture and achieved significant speedup comp

145 The output is structured similar to that of BLAST, with the list of detected homologs sorted by E-va

146 The use of BLAST at the point of care across 3 hospital ASPs result

147 ssing interface) applied in newer versios of BLAST are not adequate for processing these sequences in

148 als received training by allergists to offer BLAST for eligible patients with infectious diseases rec

149 gned to 35,029 transcripts (35.52%) based on BLAST searches against annotation databases including GO

150 Genomic scale data can be queried based on BLAST searches, annotation keywords and gene ID searches

151 hampered by its nearly complete reliance on BLAST algorithms for identification of DNA sequences.

152 nces similar to functionally annotated ones (BLAST e-value </= 1e(-70)) increased from 40.6 to 68.8%,

153 can be queried using genome browsers and/or BLAST/PSI-BLAST servers, and it may also be downloaded t

154 gnment of rearrangement sequences by BLAT or BLAST (alignment tools) and arrives at a concise and det

155 These resources can be searched by text or BLAST, browsed, and downloaded from our project Web site

156 sters of specific genes through key words or BLAST.

157 to search genomic data in FlyBase, using our BLAST server and the new implementation of GBrowse 2, as

158 ctor, an online predictor, which outperforms BLAST, PSI-BLAST and HMMER on predicting the effectors o

159 ye to extreme parallelism, enabling parallel BLAST calculations using >16 000 processing cores with a

160 ar to Nagie oko (Nok), the authors performed BLAST searches of the zebrafish genome with the Nok amin

161 A PHIB-BLAST search function is provided and a link to PHI-Cant

162 utility was integrated and a phosphopeptide BLAST browser was implemented to allow users to query th

163 Bio301 includes regular EST preprocessing, BLAST similarity search, gene ontology (GO) annotation,

164 ote services for on-the-fly BLAST and Primer BLAST analyses, graphical interfaces for configuring use

165 Primer-BLAST allows users to design new target-specific primers

166 Primer-BLAST also supports placing primers based on exon/intron

167 Primer-BLAST offers flexible options to adjust the specificity

168 ce primer design programs Primer3 and Primer-BLAST and achieved a lower primer cost per amplicon base

169 y Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Electronic PCR, OrfFinder, Splign, ProSpl

170 y Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, Prot

171 We present a new software tool called Primer-BLAST to alleviate the difficulty in designing target-sp

172 Protein BLAST analyses first demonstrate that the FMRP amino aci

173 Protein BLAST analysis confirmed that the chosen peptide markers

174 database content, incorporation of a protein BLAST (blastp) tool for finding protein sequence matches

175 powered by compressively accelerated protein BLAST (CaBLASTP), which are significantly faster than an

176 By protein BLAST, ORF1 and ORF2 were most homologous to the replica

177 Protein structures defined using protein BLAST predict that the bovine LILR family comprises seve

178 genomes do not encode typical Atg1 proteins: BLAST and HMMER queries matched only with the kinase dom

179 cBARBEL provides BLAST-based, fuzzy and specific search functions, visual

180 omparison is made between our method and PSI BLAST.

181 f PFM is shown to be better than that of PSI BLAST when sequence matching is comparable, based on a c

182 It is also shown that PFM outperforms PSI BLAST in informatically challenging targets.

183 ich therefore cannot be identified using PSI BLAST), but similarity of physical property distribution

184 PSI-BLAST homology detection revealed reciprocal homology wi

185 PSI-BLAST makes two types of errors: alignments to non-homol

186 PSI-BLAST, GLOBAL, HMMER and RPS-BLAST provided examples of

187 A PSI-BLAST analysis identified a potential H. pylori FliO pro

188 A PSI-BLAST search found over 150 full length and over 90 half

189 nd iteration to the final iteration of a PSI-BLAST search, calculates the figure of merit for each 'o

190 s existing results already produced in a PSI-BLAST search.

191 We present an add-on to BLAST and PSI-BLAST programs to reorder their hits using pairwise stat

192 re regions, against COMPASS, HHalign and PSI-BLAST, using structure superpositions and comprehensive

193 ools, including HHblits, DELTA-BLAST and PSI-BLAST.

194 he state-of-the-art performance, such as PSI-BLAST, HHblits and ProtEmbed.

195 line predictor, which outperforms BLAST, PSI-BLAST and HMMER on predicting the effectors of G protein

196 cance, along with the advantage of BLAST/PSI-BLAST in terms of speed.

197 eried using genome browsers and/or BLAST/PSI-BLAST servers, and it may also be downloaded to perform

198 rotein sequence search programs (BLASTP, PSI-BLAST and FASTM).

199 enting HOE improves selectivity for both PSI-BLAST and PSI-Search, but PSI-Search has ~4-fold better

200 ultiple sequence alignments generated by PSI-BLAST.

201 Consequently, PSI-BLAST, the most widely used method to detect remote evol

202 ESG outperforms conventional PSI-BLAST and the protein function prediction (PFP) algorith

203 region contains a non-homologous domain, PSI-BLAST can incorporate the unrelated sequence into its po

204 We used exhaustive PSI-BLAST and TBLASTN searches across 774 bacterial genomes

205 on position, cleans erroneously extended PSI-BLAST alignments to generate better profiles.

206 However, PSI-BLAST's performance is limited by the fact that it relie

207 osition-specific gap penalties in Hybrid PSI-BLAST.

208 turn, improves the accuracy of iterative PSI-BLAST searches.

209 hat uses input information comprising of PSI-BLAST 1 profiles of residue pairs, pairwise distance and

210 ess the full power of the combination of PSI-BLAST and consensus sequences.

211 We have characterized a novel type of PSI-BLAST error, homologous over-extension (HOE), using embe

212 ntly observed in the later iterations of PSI-BLAST searches.

213 tschul statistics for sensitivity and on PSI-BLAST (and other) heuristics for speed.

214 e method, PROPER, that uses a permissive PSI-BLAST approach to predict promiscuous activities of meta

215 bining four state-of-the-art predictors (PSI-BLAST, HHblits, Hmmer, and Coma) via the rank aggregatio

216 uracy, which motivates its use to refine PSI-BLAST results, since PSI-BLAST also constructs a positio

217 NCBI's PSI-BLAST utilizes iterative model building in order to bett

218 ed using local and semi-global searches, PSI-BLAST searches, and SCOP and CATH classifications.

219 ot extending previously found sequences, PSI-BLAST specificity improves 4-8-fold, with little loss in

220 s use to refine PSI-BLAST results, since PSI-BLAST also constructs a position-specific substitution m

221 arch has ~4-fold better selectivity than PSI-BLAST and similar sensitivity at 50% and 60% family cove

222 sequence search, using SSEARCH, with the PSI-BLAST profile construction strategy.

223 Notably, this improvement to PSI-BLAST comes at minimal computational cost as SIB-BLAST u

224 hat utilizes the E-values from these two PSI-BLAST iterations to obtain a figure of merit for rank-or

225 a nearest neighbor classifier that uses PSI-BLAST similarity scores.

226 Comparison with PSI-BLAST in predicting protein function in the twilight zon

227 Iterative similarity searches with PSI-BLAST position-specific score matrices (PSSMs) find many

228 In addition, users can download raw BLAST results for all or user-selected comparisons.

229 Reciprocal BLAST best hits yielded 8,785 sequences that are ortholo

230 ometry (LC-MS/MS) experiments and reciprocal BLAST, we conducted a fly-human cross-species comparison

231 design features for SNP genotyping, a remote BLAST window to NCBI databases, and remote sequence retr

232 PSI-BLAST, GLOBAL, HMMER and RPS-BLAST provided examples of using the TAP-k and pooled RO

233 reads to protein families directly using RPS-BLAST against COG and Pfam databases and indirectly via

234 ns of protein query sequences, utilizing RPS-BLAST to rapidly identify putative matches.

235 A large-scale BLAST score ratio (LS-BSR) analysis was further applied

236 he aTRAM pipeline uses a reference sequence, BLAST, and an iterative approach to target and locally a

237 little to no overhead with respect to serial BLAST.

238 A SIB-BLAST web server has been established for investigators

239 T comes at minimal computational cost as SIB-BLAST utilizes existing results already produced in a PS

240 Simple BLAST searches may reveal homology to a known toxin, whe

241 otation data sets are combined into a single BLAST server that allows users to select and combine seq

242 to perform species- and experiment-specific BLAST searches for a single gene, a list of genes, annot

243 as a standard sequence alignment technique, BLAST.

244 beta-lactam allergy skin testing (BLAST) is recommended by antimicrobial stewardship progr

245 roteins where FunFHMMer performs better than BLAST, Pfam and CDD.

246 ey are often orders of magnitude faster than BLAST in practical applications, though sensitivity to d

247 The BLAST meetings represent a field that has its roots in c

248 s of simulated viromes indicate that all the BLAST tools, followed by MetaVir and VMGAP, are more rel

249 Furthermore, although the BLAST program has been widely used for primer target det

250 General purpose tools, such as the BLAST program, have only limited use for such tasks, as

251 nhance the database search capabilities, the BLAST and BLAT search tools have been integrated with th

252 Currently, the BLAST algorithm utilizes a query-indexed approach.

253 reases, more researchers are downloading the BLAST program for local installation and performing larg

254 popular homology-search tools including the BLAST and FASTA suites.

255 ogram relies on NCBI utilities including the BLAST software and Taxonomy database and is easily manip

256 In order to implement the new method, the BLAST source code was modified to allow the researcher t

257 plications are custom implementations of the BLAST program optimized to search specialized data sets.

258 plications are custom implementations of the BLAST program optimized to search specialized data sets.

259 plications are custom implementations of the BLAST program optimized to search specialized data sets.

260 However, comparison of the BLAST results for each isolate for both regions revealed

261 evaluation from the empirical data set, the BLAST alignment of the probe sequences to a recent revis

262 Here, we describe these improvements to the BLAST report, discuss design decisions, describe other i

263 owever, no single isolate identified through BLAST carried all three SNPs simultaneously.

264 We present an add-on to BLAST and PSI-BLAST programs to reorder their hits using

265 t achieved a ~20-90-fold speedup relative to BLAST while still achieving similar levels of sensitivit

266 d speed, operating at sensitivity similar to BLAST, accuracy of ssearch and speed of MegaBLAST.

267 es can be Basic Local Alignment Search Tool (BLAST) against the UniProt Knowledgebase (UniProtKB) to

268 cture for Basic Local Alignment Search Tool (BLAST) Algorithm is proposed.

269 The Basic Local Alignment Search Tool (BLAST) is a fundamental program in the life sciences tha

270 Basic Local Alignment Search Tool (BLAST) is a sequence similarity search program.

271 The Basic Local Alignment Search Tool (BLAST) is one of the most popular and fundamental alignm

272 The Basic Local Alignment Search Tool (BLAST) is one of the most widely used bioinformatics too

273 The Basic Local Alignment Search Tool (BLAST) website at the National Center for Biotechnology

274 owse) and Basic Local Alignment Search Tool (BLAST), YersiniaBase also has in-house developed tools:

275 Our biophotonic laser-assisted surgery tool (BLAST) generates an array of microcavitation bubbles tha

276 performance of various bioinformatic tools (BLAST, MG-RAST, NBC, VMGAP, MetaVir, VIROME) for analysi

277 acterial Locomotion and Signal Transduction (BLAST).

278 ctrometry, in conjunction with a translating BLAST (tBLASTn) search, i.e., comparing the MS/MS-determ

279 Researchrs use BLAST for processing these sequences.

280 We used BLAST analyses of NS5B partial sequences to establish th

281 complementary strengths of most widely used BLAST-based function prediction methods, rarely used in

282 GSP uses BLAST to extract homeologous sequences of the subgenomes

283 The Seq2Ref server uses BLAST to detect proteins homologous to a query sequence

284 o 100,000 years and output is analyzed using BLAST (Basic Local Alignment Search Tool) alignment and

285 These trancripts were annotated using BLAST search against the Aracyc, Swiss-Prot, TrEMBL, gen

286 bovine LILR were initially identified using BLAST and BLAT software.

287 one peptide, LHP) has been identified, using BLAST and Clustal W analysis, to detect antibody of LH (

288 se and are also available for searches using BLAST.

289 ndrograms/trees from protein sequences using BLAST.

290 ntigs and singletons, which we annotated via BLAST search of chicken and human databases.

291 (AC) or the ACs of its homologs obtained via BLAST.

292 Users can search P2CS via BLAST, adding hits to their cart, and homologous protein

293 tor, a quantitative trait loci (QTL) viewer, BLAST databases and gene pages.

294 Similar to the way BLAST enables cross-species comparison of sequence data,

295 d 47.4% accuracy on experimental data (where BLAST achieved 34.0%).

296 g four different measures in comparison with BLAST, Prior, and GOtcha.

297 nd ESG are also discussed in comparison with BLAST.

298 and custom Perl scripts in conjunction with BLAST searches and available gene annotation information

299 Sequence similarity searches performed with BLAST, SSEARCH and FASTA achieve high sensitivity by usi

300 All intergenic regions were analyzed by WU-BLAST to examine conservation levels relative to species