ライフサイエンスコーパス: short sequence

1 racy on known prokaryotic genomes split into short sequences.

2 hallenge to sequence comparison not posed by short sequences.

3 highly variable, particularly when based on short sequences.

4 m this behavior can be considerable even for short sequences.

5 approximation substantially for all but very short sequences.

6 e eliminated because of their low quality or short sequences.

7 ntiate single nucleobases and amino acids in short sequences.

8 eferentially restricts recombination between short sequences.

9 criptome often produce more than 200 million short sequences.

10 is that they adopt defined conformations in short sequences.

11 We then repeated this analysis for short sequences (100-, 150-, 200- and 250-base reads) re

12 leavage sequences exhibit no homology, and a short sequence (7 amino acids) from APP that when placed

13 ene fragment contains several repetitions of short sequences, a careful optimization of the PCR condi

14 inding, but that RNA binding also requires a short sequence adjacent to the N terminus of the central

15 A but notably does require the presence of a short sequence adjacent to the target sequence within th

16 A central region (520-830) and a short sequence adjacent to the zinc cluster DNA-binding

17 Furthermore, antibody recognition of a short sequence (amino acids 92 to 125) of the C2 region

18 ct, we compared the distribution patterns of short sequences among the six categories of SNPs.

19 Here, we tested the effect of deleting the short sequence and/or the poly(U) tract from pGBB; infec

20 y identifies more than 90% of base-pairs for short sequences and 80% overall.

21 ern blotting of small RNAs is biased against short sequences and develop a protocol that removes this

22 Short sequences and/or accurate mass measurements combin

23 t one order of magnitude when searching with short sequences, and improve the alignment of proteins c

24 d for the first time includes information on short sequence- and structure-based RNA motifs present w

25 We found that a short sequence ( approximately 55 bases) in the 5' leade

26 These epitope hotspots comprised relatively short sequences ( approximately 20-80 aa in length) that

27 These short sequences are about 21 nt in length, and when synt

28 These short sequences are conserved, as other FBF-binding prot

29 In order to determine whether these short sequences are targets for antibodies involved in A

30 s inhibitor specificity domain lies within a short sequence at the carboxyl terminus of the catalytic

31 s directly to several endocytic proteins via short sequences based on the consensus residues LLDLD.

32 sidues 232, 234, 262 and 265, and connects a short sequence before the first helix with the tight tur

33 Most BIR domains bind short sequences beginning with alanine, and in this mann

34 probability of mutational configurations in short sequence blocks under a simple bottleneck model.

35 c models from configurations of mutations in short sequence blocks.

36 y counting mutations in frequency classes in short sequence blocks.

37 We found that very short sequences bound in the genome by Crx activated tra

38 We prepared site-specific CTDs within a short sequence bracketed by strong nucleosome-positionin

39 e basic leucine zipper domain of c-Jun and a short sequence close to the N terminus of Smad3 mediate

40 attB is a short sequence composed of one binding site for XerC and

41 ring a strong limb enhancer, we identified a short sequence conserved in therian mammals and capable

42 levels of sequence similarity in relatively short sequences constituting the functionally important

43 ng seed plants, each characterized by a very short sequence containing a central putative zinc finger

44 tion assays showed that AP-2alpha occupies a short sequence containing center 1.

45 cell survival and blocks apoptosis, while a short sequence containing LKKTETQ, the central actin-bin

46 A hypothesis is proposed in which short sequences containing just the reverse transcriptas

47 This short sequence contains binding sites for homeodomain tr

48 In this study, we identified a short sequence covering residues Lys-20 to Ala-52 in G0S

49 However, deviations from the model for short sequence deletions suggest that RAM contains seque

50 The trafficking effects of short sequences differing in PDZ and SAP97 binding were

51 Multiple short sequences dispersed along the macroH2A1 histone do

52 e currently often limited to single steps or short sequences due to the complexity involved with oper

53 A short sequence element in the mouse bcl-x promoter that

54 The argument for the importance of short sequence elements hinged on the relatively-high ac

55 e the direct recognition of D and KEN boxes, short sequence elements in substrates of the anaphase-pr

56 Very short sequence elements or microhomologies were also ide

57 the internal transcribed spacers are several short sequence elements which are identical between the

58 ysis suggested, dependent on the presence of short sequence elements with high amyloid-forming potent

59 differential binding to 8.4 million distinct short sequence elements.

60 ) duplication with long repeats separated by short sequence elements: AB*(CD)*(CD)*E (* = a few bases

61 Moreover, a short sequence encompassing the three footprints was fou

62 bility to quantify homopolymeric runs, and a short sequencing example of sections of the wild-type an

63 infectious GBV-B clone (pGBB) has a proximal short sequence followed by a poly(U) tract and a 3' term

64 describe an algorithm, Local Distribution of Short Sequences for Prokaryotes (LDSS-P), to identify co

65 protein, and show that a region containing a short sequence found in several G-actin binding proteins

66 nd that for each genome, the majority of its short sequence fragments have highly similar barcodes wh

67 ell, known as RNA-Seq, generates millions of short sequence fragments in a single run.

68 Mapping the vast quantities of short sequence fragments produced by next-generation seq

69 Crucially, our method performs well for short sequence fragments, facilitating evaluation of mic

70 , sulfoxide, and sulfone, were prepared by a short sequence from the ethylene glycol ketal of hydroco

71 First, the host can specifically incorporate short sequences from invading genetic elements (virus or

72 raurelia must eliminate approximately 60,000 short sequences from its genome to generate uninterrupte

73 interest," leaving only the desired gene and short sequences from the recombinase recognition site.

74 was localized within gamma370-381, with two short sequences, gamma370ATWKTR375 and gamma376WYSMKK381

75 stereochemistry then became viable through a short sequence highlighted by an aldol condensation with

76 ce of TdT are more uniform due to the use of short sequence homologies between the V, D, and J genes.

77 evealed excessive deletions, frequent use of short sequence homologies, and unusually long palindromi

78 ve been reported that characteristically use short-sequence homologies at the DNA ends to facilitate

79 ne and preferential repair is seen only in a short sequence immediately downstream of the transcripti

80 kinase I (CaMKI) through interactions with a short sequence in its regulatory domain.

81 NA near the leading edge is facilitated by a short sequence in the 3' untranslated region, the "zip c

82 core ADAMTS13-binding site is contained in a short sequence in the A2 domain, but other domains affec

83 The second is a short sequence in the hairy2 3' untranslated region (UTR

84 downregulation fails due to a mutation in a short sequence in the lin-28 3' UTR that is complementar

85 ing site for alpha-actinin-2 was mapped to a short sequence in the membrane-proximal region of ADAM12

86 Here we present data that define a short sequence in the N-terminal region of PTEN required

87 A short sequence in the RT domain was localized that was d

88 on between a hydrophobic patch in Clb5 and a short sequence in the substrate (the RXL or Cy motif).

89 nts has led to the generation of millions of short sequences in a single run.

90 ays a role in limiting recombination between short sequences in eukaryotic cells.

91 We found three conserved short sequences in RRM3 that were essential for the inte

92 Some homology was found with short sequences in the expressed sequence tag (EST) data

93 The talin F3 domain also binds to short sequences in the layilin cytoplasmic domain, and h

94 Two short sequences in the N and C termini were found to be

95 kinase, C-Src, undergoes splicing to insert short sequences in the SH3 domain to yield N1- and N2-Sr

96 We found that CpG-containing short sequences, in general, had more representation in

97 The key step of this short sequence is a [4 + 2]/retro-[4 + 2] cycloaddition

98 This short sequence is not found in Rabphilin3 and is entirel

99 HIV-long terminal repeat indicates that this short sequence is sufficient to promote HIV infection.

100 ntains a third phiXXphiphi motif (LX3) and a short sequence, KQL, which has similarity to a region in

101 In contrast, short sequences lacking symmetrical cytosines were less

102 Dark proteins also had short sequence length, low evolutionary reuse, and few k

103 t lineage in the fetal pancreas depends on a short sequence located approximately 2 kb upstream of th

104 cting region of Hdm2 is also composed of two short sequences located in the central acidic domain, be

105 A short sequence, located between the A14L and A15L open r

106 From the overlap of these short sequences, long contiguous sequences that encode s

107 These short sequences may have facilitated nonhomologous recom

108 arget mimic (STTM), which is composed of two short sequences mimicking small RNA target sites, separa

109 They highlight the significant effect that short sequence mismatches can have upon microarray hybri

110 In contrast, a short sequence (mjTFIIB A81-K89) between these two clust

111 inger array that, in humans, can recognize a short sequence motif associated with hot spots, with bin

112 discovered that all Paramyxovirinae share a short sequence motif in their first 40 amino acids, whic

113 rs429358 that defines APOE4 is located in a short sequence motif repeated several times within exon

114 Intriguingly, the p9 sequence contains a short sequence motif that is similar to a surface-expose

115 In the last case, short sequence motifs (termed late domains) within human

116 strong correlation between the inclusion of short sequence motifs and the activity level of an oligo

117 known as WD40 and beta-transducin repeats), short sequence motifs appearing in clusters of 4-16 foun

118 Short sequence motifs are an important class of models i

119 for multiple scales, the spatial patterns of short sequence motifs associated with indel mutagenesis.

120 EST database searches with short sequence motifs shared by known phosphate transpor

121 e been proposed to specify FMRP binding, the short sequence motifs TGGA and GAC were corroborated, an

122 Transcription factors (TFs) recognize short sequence motifs that are present in millions of co

123 and predicted secondary structures revealed short sequence motifs that mediate binding to the She co

124 Bcl-2 homology 3 (BH3) domains are short sequence motifs that mediate nearly all protein-pr

125 ectronic search based on the conservation of short sequence motifs within the variable region of immu

126 proteins, which contain multiple repeats of short sequence motifs, form a large but seldom-studied g

127 and the frequencies of occurrence of several short sequence motifs.

128 codons when the ribosome encounters specific short sequence motifs.

129 We identified 2 short-sequence motifs in human NTCP that were required f

130 , however, the significance and scope of the short-sequence motifs in these cellular events is not we

131 Concurrent with this progress, fast (or short sequence) MRI represents an emerging technology th

132 The approach involves cloning a short sequence of a targeted plant gene into a viral del

133 A short sequence of amino acids at the C terminus of ZFP80

134 We localized the DHBV 5E element to a short sequence of approximately 30 nucleotides that is 1

135 s to acidic phospholipids in vitro through a short sequence of basic and hydrophobic amino acids, BH

136 A short sequence of catalytic C(sp(3))-H amination-cycliza

137 If the template strand contains a short sequence of G residues, it is copied in the presen

138 We report that a short sequence of ICP0 is similar to a sequence in the a

139 the regions responsible for the binding to a short sequence of Kidins220/ARMS, termed KLC-interacting

140 t(Mx8) terminator sequence, in addition to a short sequence of Mx8 DNA downstream of trnD.

141 at a raft-localizing marker, consisting of a short sequence of positively charged amino acid residues

142 iarylacrylonitriles to be prepared in a very short sequence of reactions.

143 A well studied short sequence of the p53 transactivation domain, p53(15

144 S cysteine desulfurase and the presence of a short sequence of ThiI in these bacteria pointed to mech

145 Previous work demonstrated that a short sequence of U1A protein is essential for autoregul

146 were constructed by substituting one or more short sequences of alpha3(IV)NC1 at the corresponding po

147 little is known about the behavior of these short sequences of amino acids within cells, particularl

148 an localize the sites of DNA binding to very short sequences of amino acids.

149 on initiation region of target mRNAs through short sequences of complementarity, blocking their ribos

150 es has lead to their use in testing specific short sequences of DNA as a "barcode" for the identifica

151 ants heard, read, or viewed demonstration of short sequences of instructions, and recalled either by

152 Riboswitches are short sequences of messenger RNA that can change their s

153 hown that not only single residues, but also short sequences of non-proline residues can adopt the P(

154 ation of such a first-in first-out buffer of short sequences of spike patterns includes noise and dif

155 e strong evidence that they are representing short sequences of states.

156 Many peptides contained short sequences of two to three acidic residues.

157 four genomic breakpoints that are joined by short sequences of unknown origin.

158 thin the rhythm domain for the processing of short sequences of up to seven tones.

159 strategy was applied to the synthesis, in a short sequence, of a constrained mimetic of the privileg

160 We quantitatively evaluate their impact when short-sequence oligonucleotide arrays are applied (Affym

161 ed kojic acid-tripeptides, mimosine-FFY, and short-sequence oligopeptides at inhibiting mushroom tyro

162 However, mutants lacking either the short sequence or the poly(U) tract were viable.

163 A short sequence overlapping the primer binding site acts

164 In one proposed mechanism, short sequences (packaging sites) within the genomic RNA

165 Short sequence patterns frequently define regions of bio

166 A search for short sequence patterns revealed a number of motifs whic

167 of translation by variation in the number of short-sequence pentanucleotide repeats (CAAAA) located i

168 to the cell interior is mediated by specific short-sequence peptide signals within the cytoplasmic do

169 ucleolar localization were observed with the short sequence PFVYLI, but not with SIPPEVKFNK, and the

170 ese results suggest a specific function of a short sequence present in the N-terminal domain in contr

171 ing effort is best focused on gathering more short sequences rather than fewer longer ones, provided

172 methods use massively parallel detection of short sequencing reactions, making them ideal for the an

173 In addition, de novo short sequence read assembly strategy identified several

174 bserved, mostly related to the limitation of short sequence read assembly.

175 ease risk cutoffs are close to or beyond the short sequence read length of 100 to 150 bases.

176 ements due to inherent sequencing errors and short sequence read lengths.

177 cing has heretofore been used for generating short sequence reads (1-100 nucleotides) because certain

178 optimal construction of these genomes using short sequence reads are key to this process.

179 jor technical hurdle lies in the need to map short sequence reads back to their correct locations in

180 Here, we show that short sequence reads can be aligned to a genome assembly

181 Second, relatively short sequence reads contain little to no haplotype info

182 entify viral recombination directly from the short sequence reads created by next-generation sequenci

183 repetitive DNA, which makes the assembly of short sequence reads difficult.

184 In these assays, short sequence reads enriched for loci of interest are m

185 Typically, short sequence reads from ChIP-Seq are mapped to a refer

186 Metatranscriptomic analysis of the short sequence reads identified a 10.5-kb sequence from

187 d and used to measure the number of matching short sequence reads in feces from the 92 animals in the

188 lleles with single base pair resolution from short sequence reads is challenging due to several sourc

189 Traditional techniques used for assembly of short sequence reads produced by deep sequencing, such a

190 h-throughput sequencing technologies produce short sequence reads that can contain phase information

191 we describe using the overlap of paired-end, short sequence reads to identify error-prone reads in ma

192 erited variation of microsatellite loci from short sequence reads without paired-end information.

193 we present SISSRs (Site Identification from Short Sequence Reads), a novel algorithm for precise ide

194 verage and B-allele frequencies, from mapped short sequence reads, and we assess both the method's po

195 ntion to what is lost by sole application of short sequence reads.

196 h PML without the bias caused by assembly of short sequence reads.

197 robial community, based on classification of short sequence reads.

198 us providing a framework for assembly of the short sequence reads.

199 as their relative abundances, directly from short sequence reads.

200 tions is still challenging with low-coverage short sequence reads.

201 ta typically consists of tens of millions of short sequenced reads from different transcripts.

202 heeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequenc

203 tep in analyzing WGS and WES data is mapping short sequencing reads back to the reference genome.

204 terpretation is complicated by the fact that short sequencing reads can match multiple organisms and

205 he AB SOLiD technology generates millions of short sequencing reads in color-space; that is, the raw

206 A novel and robust method to detect CNV from short sequencing reads is proposed in this study.

207 a. the transcript assembly problem) from the short sequencing reads produced by RNA-seq protocol play

208 Many programs for aligning short sequencing reads to a reference genome have been d

209 h RNA-Seq requires the mapping of relatively short sequencing reads to a reference genome or transcri

210 es) that iteratively aligns deep coverage of short sequencing reads to correct errors in reference ge

211 mplexities involved in properly apportioning short sequencing reads to highly repetitive regions of t

212 fragments retains long-range information in short sequencing reads.

213 olymorphisms into viral haplotypes from very short sequencing reads.

214 e identification of genomic alterations from short sequencing reads.

215 n confound SNP-typing microarrays or mapping short-sequence reads and therefore must be accounted for

216 In many workflows, each of the short sequences ("reads") resulting from a sequencing ru

217 erforming 'binning' or 'windowing' on mapped short sequences ('reads') is critical to extract genomic

218 human homologue FEN1 complement the elevated short-sequence recombination (SSR) phenotype of a rad27-

219 ength, indicating that they are required for short-sequence recombination (SSR).

220 ed Ty1 cDNA, which leads to higher levels of short-sequence recombination and Ty1 retrotransposition.

221 romyces cerevisiae genome by increasing both short-sequence recombination and Ty1 retrotransposition.

222 Two homologous short sequences, referred to as the A and B boxes, near

223 enetic methods, with the rest involving very short sequence regions (15 to 30 nt).

224 enerating accurate structure models for even short sequences remains difficult.

225 We describe a multilocus short sequence repeat (MLSSR) sequencing approach for th

226 subsp. paratuberculosis, regardless of their short sequence repeat (SSR) genotype, induced similar gl

227 of a recently identified M. paratuberculosis short sequence repeat (SSR) region enabled the different

228 We identified 87 short sequence repeat loci within the genome of the M. t

229 variation in two of the most discriminatory short sequence repeat loci, i.e., mononucleotide G and t

230 The short sequence repeat locus is located at position - 55

231 We conclude that this short sequence repeat motif is located upstream of the d

232 Short sequence repeat polymorphisms for the human plasma

233 Coagulase gene (coa) short sequence repeat region sequencing was used to meas

234 ve samples using two polymorphic (G and GGT) short sequence repeat regions identified varying levels

235 n A and, more specifically, the Xr domain, a short sequence-repeat region encoded by DNA that consist

236 Using a multilocus short-sequence-repeat technique, we found 15 different s

237 improve the alignment of proteins containing short sequences repeated in tandem.

238 We analyzed the multilocus short sequence repeats (SSRs) of 211 and 56 isolates of

239 was aimed to determine whether the number of short sequence repeats (SSRs) present in the polymorphic

240 ations identified a subset of 11 polymorphic short sequence repeats (SSRs), with an average of 3.2 al

241 Analysis of short sequence repeats of Mycobacterium avium subsp. par

242 al phenotypic variation via HFMs, deletions, short sequence repeats, and single-nucleotide polymorphi

243 half of the recent gains are associated with short sequence repeats, suggesting an origin via repair

244 st evidence of transcriptional regulation by short-sequence repeats in a Gram-positive organism.

245 The PTGS-competent short sequences resulted in similar patterns of methylat

246 In the accompanying article, three short sequence segments (nucleic acid binding sequences

247 Beacon 10 also shared short sequence segments with other published BoNT aptame

248 At short sequence separation the energy functions are assoc

249 emphasis has been given to the functions of short-sequence signal motifs responsible for the itinera

250 zoite promoters led to the identification of short sequence spans that are involved in control of bra

251 he binding of transcription factors (TFs) to short sequence-specific DNA motifs, usually located at t

252 unctions at most TATA-less genes, recognizes short sequence-specific promoter elements in metazoans,

253 A short sequence stretch within this exon has the unique f

254 data structure to find exact matches between short sequence strings (k-mers) and an MLST allele libra

255 I-sites motifs are short sequence/structure motifs that populate the protei

256 vity than previous methods, performs well on short sequences such as those produced by the 454 Life S

257 ulatory module: (1) Positive elements (PEs), short sequences sufficient for strong muscle expression

258 a fragmenting enzyme (for example, NlaIII), short sequence tags can be obtained and uniquely mapped

259 ture sequencing (MPSS) generates millions of short sequence tags corresponding to transcripts from a

260 Digital karyotyping uses short sequence tags derived from specific genomic loci t

261 fficient sequential method for concatenating short sequence tags for any serial analysis of gene expr

262 In this remarkable pathway, short sequence tags from invading genetic elements are a

263 ch involves the isolation and enumeration of short sequence tags from specific genomic loci.

264 ene expression level, generating millions of short sequence tags per library.

265 h a view to scaling ecological analyses, the short sequence, taxonomic resolution and accurate automa

266 in the deleted peptide, we have identified a short sequence, termed the chromatin-binding motif (CBM)

267 yrimidine ribonucleotides can be formed in a short sequence that bypasses free ribose and the nucleob

268 particularly near the SH2 interface and the short sequence that connects SH3 to SH2, implying greate

269 Surprisingly, the Nanog homeodomain, a short sequence that contains the only recognizable conse

270 among the RGS-RhoGEFs, PDZ-RhoGEF contains a short sequence that localizes the protein to the actin c

271 Here, we used mutagenesis to identify a short sequence that supports long-term expression.

272 nal analysis, we first created a database of short sequences that are highly conserved among 12 Droso

273 ily of proteins, and it includes a number of short sequences that are related to SUMO interaction mot

274 develop diagnostic DNA signatures, which are short sequences that are sufficient to uniquely identify

275 elements to the E6/E7 region and identified short sequences that could serve as binding sites for tr

276 of TcdB (amino acid residues 1753-1851) for short sequences that function as cell-penetrating peptid

277 ge-display technologies, in the selection of short sequences that have affinity to (noble) metals, se

278 The proteins shared a short sequence, the Lag1 motif, and a similar transmembr

279 Because the probes recognize short sequences, they encounter multiple cognate sites o

280 entation, SeqMap can map tens of millions of short sequences to a genome of several billions of nucle

281 SeqMap is a tool for mapping large amount of short sequences to the genome.

282 onformation, resulting in sequestration of a short sequence tract otherwise required for downstream g

283 concomitant use of the multiple fragments of short sequence typically available from methods of tande

284 Short sequences were able to initiate PTGS of an endogen

285 gment) of the genome while repair-initiating short sequences were distributed more uniformly in gamma

286 The results revealed that the short sequences, which contained at least one CpG dinucl

287 ls have a limited ability to recognize these short sequences, which range in length up to 25 bp.

288 y, sequencing runs produce a large number of short sequences whose exact origin is unknown.

289 re murine oocytes revealed the presence of a short sequence with partial homology to a cyclin-like hu

290 Among such signals are short sequences with high AU contents that constitute re

291 Because we found numerous short sequences with IRES activity, there might be many

292 vidual sites under selection when applied to short sequences with low divergence.

293 To identify other short sequences with similar properties, we designed a s

294 nverse proportion to the sequence length for short sequences, with change to slow exponential decay f

295 A short sequence within PACS-1 that is essential for bindi

296 hagocyte integrin Mac-1 (CD11b/CD18) and one short sequence within the fibrinogen D domain (gamma 190

297 Previous work has shown that Gol, a short sequence within the major capsid protein gp23, act

298 We identified short sequences within each variant that determine the e

299 Recent evidence suggests that specific short sequences within exons help in defining these boun

300 Analyses of mutations indicated that 2 short sequences within the element, about 15 base pair a