Abstract:
:One-Block CYRCA is an automated procedure for identifying multiple-block alignments from single block queries (http://bioinfo.weizmann.ac.il/blocks/OneCYRCA). It is based on the LAMA and CYRCA block-to-block alignment methods. The procedure identifies whether the query blocks can form new multiple-block alignments (block sets) with blocks from a database or join pre-existing database block sets. Using pre-computed LAMA block alignments and CYRCA sets from the Blocks database reduces the computation time. LAMA and CYRCA are highly sensitive and selective methods that can augment many other sequence analysis approaches.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Frenkel-Morgenstern M,Singer A,Bronfeld H,Pietrokovski Sdoi
10.1093/nar/gki488keywords:
subject
Has Abstractpub_date
2005-07-01 00:00:00pages
W281-3issue
Web Server issueeissn
0305-1048issn
1362-4962pii
33/suppl_2/W281journal_volume
33pub_type
杂志文章abstract::Alternative splicing is the primary source of proteome complexity in metazoans and its regulation shapes the proteome in response to shifting physiological requirements. We developed a bichromatic splicing reporter that uses a peculiar feature of some fluorescent protein coding regions to express two different fluores...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl967
更新日期:2006-01-01 00:00:00
abstract::eIF4E-binding proteins (4E-BPs) regulate translation of mRNAs in eukaryotes. However the extent to which specific mRNA targets are regulated by 4E-BPs remains unknown. We performed translational profiling by microarray analysis of polysome and monosome associated mRNAs in wild-type and mutant cells to identify mRNAs i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq686
更新日期:2010-12-01 00:00:00
abstract::In most cells, transcriptionally inactive heterochromatin is preferentially localized in the nuclear periphery and transcriptionally active euchromatin is localized in the nuclear interior. Different cell types display characteristic chromatin distribution patterns, which change dramatically during cell differentiatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz123
更新日期:2019-05-21 00:00:00
abstract::RNA sequencing (RNA-Seq) is a powerful tool for analyzing the identity of cellular RNAs but is often limited by the amount of material available for analysis. In spite of extensive efforts employing existing protocols, we observed that it was not possible to obtain useful sequencing libraries from nuclear RNA derived ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv213
更新日期:2015-06-23 00:00:00
abstract::Although many tools have been developed to analyze small RNA sequencing (sRNA-Seq) data, it remains challenging to accurately analyze the small RNA population, mainly due to multiple sequence ID assignment caused by short read length. Additional issues in small RNA analysis include low consistency of microRNA (miRNA) ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx999
更新日期:2017-12-01 00:00:00
abstract::Transcription factors are important gene regulators with distinctive roles in development, cell signaling and cell cycling, and they have been associated with many diseases. The ConTra v3 web server allows easy visualization and exploration of predicted transcription factor binding sites (TFBSs) in any genomic region ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx376
更新日期:2017-07-03 00:00:00
abstract::Guanine-rich sequences are highly abundant in the human genome, especially in regulatory regions. Because guanine-rich sequences have the unique ability to form G-quadruplexes, these structures may play a role in the regulation of gene transcription. In previous studies, we demonstrated that formation of G-quadruplexe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr259
更新日期:2011-09-01 00:00:00
abstract::Short oligo(deoxynucleoside phosphorothioate)s were analyzed as a pool of individual diastereomeric species. The composition of such mixtures, determined by means of HPLC, indicates that consecutive couplings in commonly used phosphoramidite chemistry lead to increasing contents of the Rp isomer. Methods of analysis a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.3.530
更新日期:1995-02-11 00:00:00
abstract::The secondary structure of an adenovirus associated low molecular weight RNA (VAI-RNA) has been studied by partial digestion with T1-RNase and S1-endonuclease followed by T1-fingerprint analysis. The empirical secondary structure has been compared with two computer generated models based on minimal free energy of the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.17.4239
更新日期:1981-09-11 00:00:00
abstract::UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets the formal fungal barcode-the nuclear ribosomal internal transcribed spacer (ITS) region-and offers all ∼1 000 000 public fungal ITS sequences for reference. These are clustere...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1022
更新日期:2019-01-08 00:00:00
abstract::The small subunit ribosomal RNA gene (16S rRNA) has been successfully used to catalogue and study the diversity of prokaryotic species and communities but it offers limited resolution at the species and finer levels, and cannot represent the whole-genome diversity and fluidity. To overcome these limitations, we introd...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky467
更新日期:2018-07-02 00:00:00
abstract::We have determined the NMR solution structures of the quadruplexes formed by d(TGLGLT) and d(TL4T), where L denotes LNA (locked nucleic acid) modified G-residues. Both structures are tetrameric, parallel and right-handed and the native global fold of the corresponding DNA quadruplex is retained upon introduction of th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl144
更新日期:2006-04-13 00:00:00
abstract::The nucleotide sequence of Drosophila melanogaster methionine tRNAi was determined to be: pA-G-C-A-G-A-G-U-m1G-m2G-C-G-C-A-G-U-G-G-A-A-G-C-G-U-m2G-C-U-G-G-G-C-C-C-A-U-t6A-A-C-C-C-A-G-A-G-m7G-D-m5C-C-C-G-A-G-G-A-U-C-G-m1A-A-A-C-C-U-U-G-C-U-C-U-G-C-U-A-C-C-A(OH). It differs from vertebrate initiator tRNAs in only 6 out ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.2.421
更新日期:1979-02-01 00:00:00
abstract::Yaf9 is an integral part of the NuA4 acetyltransferase and the SWR1 chromatin remodeling complexes. Here, we show that Yaf9 associates with acetylated histone H3 with high preference for H3K27ac. The crystal structure of the Yaf9 YEATS domain bound to the H3K27ac peptide reveals that the sequence C-terminal to K27ac s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1151
更新日期:2018-01-09 00:00:00
abstract::The solid phase synthesis of oligoribonucleotides using the H-phosphonate approach and the 1-[(2-chloro-4-methyl)phenyl]-4-methoxypiperidin-4-yl (Ctmp) and dimethoxytrityl (DMTr) groups, respectively, for the protection of the 2'- and 5'-hydroxy functions is described. The use of a new reagent, tris-(1,1,1,3,3,3-hexaf...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.10.3689
更新日期:1989-05-25 00:00:00
abstract::Despite two decades of study, the full scope of RNAi in mammalian cells has remained obscure. Here we combine: (i) Knockout of argonaute (AGO) variants; (ii) RNA sequencing analysis of gene expression changes and (iii) Enhanced Crosslinking Immunoprecipitation Sequencing (eCLIP-seq) using anti-AGO2 antibody to identif...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa478
更新日期:2020-07-27 00:00:00
abstract::A putative role for mammalian polynucleotide kinases that possess both 5'-phosphotransferase and 3'-phosphatase activity is the restoration of DNA strand breaks with 5'-hydroxyl termini or 3'-phosphate termini, or both, to a form that supports the subsequent action of DNA repair polymerases and DNA ligases, i.e. 5'-ph...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.19.4395
更新日期:1998-10-01 00:00:00
abstract::The primary structures of two overlapping novel alpha-tubulin cDNA clones isolated from a Macaca fascicularis testis cDNA library and the corresponding human gene are presented. Although the general structure of the human gene conforms to that of previously described mammalian alpha-tubulin genes, there is a surprisin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.1.199
更新日期:1987-01-12 00:00:00
abstract::A novel method for sequence specific double strand DNA cleavage using PNA (peptide nucleic acid) targeting is described. Nuclease S1 digestion of double stranded DNA gives rise to double strand cleavage at an occupied PNA strand displacement binding site, and under optimized conditions complete cleavage can be obtaine...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.9.2103
更新日期:1993-05-11 00:00:00
abstract::TOP mRNAs are vertebrate transcripts which contain a 5'terminal oligopyrimidine tract (5'TOP), encode for ribosomal proteins and elongation factors 1alpha and 2, and are candidates for growth-dependent translational control mediated through their 5'TOP. In the present study we show that elongation factor 2 (EF2) mRNA ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.5.995
更新日期:1997-03-01 00:00:00
abstract::During erythropoiesis in the chick, the nucleosome repeat length increases from 190 base pairs to 212 base pairs. This increase is correlated with a dramatic increase in the concentration of the red cell specific histone H5 (from 0.2 molecules per nucleosome to 1 molecule per nucleosome) and with no change in the conc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.4.1179
更新日期:1978-04-01 00:00:00
abstract::The expression of thymidine kinase in fungi, which normally lack this enzyme, will greatly aid the study of DNA metabolism and provide useful drug-sensitive phenotypes. The herpes simplex virus type-1 thymidine kinase gene ( tk ) was expressed in Neurospora crassa. tk was expressed as a fusion to N.crassa arg-2 regula...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.12.2389
更新日期:1997-06-15 00:00:00
abstract::Several fungal species, representatives of all broad groups like basidiomycetes, ascomycetes and phycomycetes, were examined for the nature of repeated DNA sequences by DNA:DNA reassociation studies using hydroxyapatite chromatography. All of the fungal species tested contained 10-20% repeated DNA sequences. There are...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/1.11.1411
更新日期:1974-11-01 00:00:00
abstract::A novel resource centre for TP53 mutations and mutants has been developed (http://p53.fr). TP53 gene dysfunction can be found in the majority of human cancer types. The potential use of TP53 mutation as a biomarker for clinical studies or exposome analysis has led to the publication of thousands of reports describing ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1033
更新日期:2013-01-01 00:00:00
abstract::To synchronize SV40 replicons, simian cells infected with a tsA mutant were restricted at 40 degrees, to complete ongoing replication and returned to 32 degrees, to activate new replicons in the presence of the DNA chain elongation inhibitor aphidicolin. Upon further incubation at 40 degrees without the drug, 3H-dT wa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.2.763
更新日期:1982-01-22 00:00:00
abstract::Insertion of the insertion sequence Is2(I) directly before the galE gene of the galactose operon results in a Gal minus phenotype (1, 2). The Gal-constitutive allele galc200 (and its deletion derivative galc200 delta 31) arise from such a Gal minus mutant by the insertion of LS2(II) DNA within the LS2(I) sequence (3)....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.16.5015
更新日期:1982-08-25 00:00:00
abstract::To confirm the activity of an initial small molecule 'hit compound' from an activity screening, one needs to probe the structure-activity relationships by testing close analogs. The multi-fingerprint browser presented here (http://dcb-reymond23.unibe.ch:8080/MCSS/) enables one to rapidly identify such close analogs am...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku379
更新日期:2014-07-01 00:00:00
abstract::Accurate maps and DNA sequences for human subtelomere regions, along with detailed knowledge of subtelomere variation and long-range telomere-terminal haplotypes in individuals, are critical for understanding telomere function and its roles in human biology. Here, we use a highly automated whole genome mapping technol...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx017
更新日期:2017-05-19 00:00:00
abstract::The TPA-inducible transcription factor AP-1, consisting of homo- or hetero-dimers of members of the Jun- and Fos-families, regulates transcription of a wide variety of genes containing the TPA response element (TRE). In P19 embryonal carcinoma (EC) cells, Jun D is the only component of AP-1 expressed, while in these c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.1.125
更新日期:1992-01-11 00:00:00
abstract::The U1 snRNP-specific protein C contains an N-terminal zinc finger-like CH motif which is required for the binding of the U1C protein to the U1 snRNP particle. Recently a similar motif was reported to be essential for in vivo homodimerization of the yeast splicing factor PRP9. In the present study we demonstrate that ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.23.4864
更新日期:1995-12-11 00:00:00