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 creates local sequence alignments by first buildin

6 BLAST is a heuristic biological sequence alignment algor

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

8 BLAST jobs that hitherto failed or slogged inefficiently

9 (BLAST presently does not permit its alignments to includ

10 BLAST provides sequence similarity searches of GenBank a

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

12 BLAST search analysis revealed that the S. flexneri 2457

13 BLAST searches and phylogenetic analyses indicate pXF-RI

14 BLAST searches indicated that the S. frugiperda rhabdovi

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

16 BLAST-based characterizations of non-ribosomal RNA seque

17 BLAST-ing these novel contigs against all publically ava

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

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

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

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

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

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

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

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

26 It can align reads to a BLAST database or a FASTA file.

27 Here, using a BLAST search for genes encoding putative CAE proteins in

28 tification algorithms require all-versus-all BLAST comparisons, which are time-consuming and memory i

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

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

31 ther NCBI resources such as Gene, dbGaP, and BLAST; and provides a platform for customized analysis a

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

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

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

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

36 enchmark has been tested using the naive and BLAST baseline methods, as well as two orthology-based m

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

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

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

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

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

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

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

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

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

46 speedup of sequence alignment tools such as BLAST.

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

48 mpared to other homolog search tools such as BLAST.

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

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

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

52 s that predict protein function, but a basic BLAST-based method is still a top contender.

53 analysis tools such as NCBI BLAST and Batch BLAST.

54 tion/association studies, bidirectional best BLAST hits, sorting signals, known databases and visuali

55 uences were binned into 1,566 different best BLAST hits (BBHs) and counted for each mouse sample.

56 using modified approaches of reciprocal best BLAST hits (RBH) and UCLUST.

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

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

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

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

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

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

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

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

65 rate compared to that of ~ 40% generated by BLAST, both at a high precision level (> 95%).

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

67 a sequence with a structure as identified by BLAST, and thus relate 3D structure to a large fraction

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

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

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

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

72 of frameshift alignments, similar to classic BLAST statistics.

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

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

75 host as the webserver, with a self-contained BLAST module leveraging NCBI Blast+ commands, or via a m

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

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

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

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

80 The VFs can also be searched by a customized BLAST sequence similarity searching program.

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

82 nnotation pipeline, Genome Workbench, dbSNP, BLAST, Primer-BLAST, IgBLAST and PubChem.

83 c genomes, Genome, BioProject, dbSNP, dbVar, BLAST databases, igBLAST, iCn3D and PubChem.

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

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

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

87 EC-BLAST has the potential to improve enzyme classification

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

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

90 New features also include enhanced BLAST search capabilities for external queries.

91 t that allow users 1) to specify and execute BLAST searches by either running on the same host as the

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

113 with greater sensitivity than non-iterative BLAST.

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

115 The LnCeVar-BLAST interface is a convenient way for users to search

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

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

118 Magic-BLAST uses innovative techniques that include the optimi

119 We introduce Magic-BLAST, a new aligner based on ideas from the Magic pipel

120 We evaluate the performance of Magic-BLAST to accurately map short or long sequences and its

121 We show that Magic-BLAST is the best at intron discovery over a wide range

122 This seed-and-extend heuristic makes BLAST extremely fast and has led to its almost exclusive

123 Moreover, BLAST searches of the public synchronized databases with

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

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

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

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

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

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

130 ch, delivers identical hits returned to NCBI BLAST.

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

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

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

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

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

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

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

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

139 BLANT is the analog of BLAST, but for networks: given an input graph, it sample

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

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

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

143 orthology determination through a series of BLAST searches, as well as phylogenetic analyses, we est

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

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

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

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

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

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

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

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

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 TIGER uses a comparative genomic, ping-pong BLAST approach, based on the principle that the IGE inte

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

164 types of "alerts" that (unlike the previous BLAST-based system) provide deterministic and rigorous f

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 line, Genome Workbench, dbSNP, BLAST, Primer-BLAST, IgBLAST and PubChem.

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

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

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

173 Protein BLAST analyses first demonstrate that the FMRP amino aci

174 Protein BLAST analysis confirmed that the chosen peptide markers

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

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

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

178 ed using a similarity search in NCBI protein BLAST program (BLASTP).

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

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

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

182 omparison is made between our method and PSI BLAST.

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

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

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

186 PSI-BLAST homology detection revealed reciprocal homology wi

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

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

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

190 andomly selected homologs sampled from a PSI-BLAST search achieves average F-Scores of ~0.3, a perfor

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

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

193 low sequence similarity identified by a PSI-BLAST search.

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

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

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

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

198 nly used sequence searching tools, BLAST/PSI-BLAST and HMMER.

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

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

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

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

203 ultiple sequence alignments generated by PSI-BLAST.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

218 HHblits3 is ~10x faster than PSI-BLAST and ~20x faster than HMMER3.

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

220 simple naive conservation approach using PSI-BLAST in many cases outperformed other methods.

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

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

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

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

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

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

227 utomatically retrieved from UniProt; replace BLAST with an alternative algorithm; or tailor the metho

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

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

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

231 BovineMine) and sequence database searching (BLAST).

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

233 little to no overhead with respect to serial BLAST.

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

235 Here, using in silico (BLAST) genome analyses, we show that the myomaker gene f

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

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

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

239 dase A gene, named here nanH1 In this study, BLAST searches predicted two additional G. vaginalis sia

240 as a standard sequence alignment technique, BLAST.

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

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

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

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

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

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

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

248 ncludes open source applications such as the BLAST+ suite, InterProScan, and several gene callers, as

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

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

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

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

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

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

255 Custom implementations of the BLAST program provide sequence-based searching of many s

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

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

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

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

260 dictions by homology-based inference through BLAST.

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

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

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

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

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

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

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

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

269 erforms a basic local alignment search tool (BLAST) search against the genome assembly for their part

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

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

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

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

274 two commonly used sequence searching tools, BLAST/PSI-BLAST and HMMER.

275 gy (GO) terms were assigned based on the top BLAST hit using Blast2GO.

276 acterial Locomotion and Signal Transduction (BLAST).

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

278 Researchrs use BLAST for processing these sequences.

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

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

281 GSP uses BLAST to extract homeologous sequences of the subgenomes

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

283 with nucleotide-to-protein alignments using BLAST.

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 ein sequence-based search is performed using BLAST to match microarray data with all available PDB st

289 se and are also available for searches using BLAST.

290 ndrograms/trees from protein sequences using BLAST.

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