Abstract:
:A fundamental problem with applying Consensus, Weight-Matrix or hidden Markov models as search tools for biosequences is that there is no way to know, from the model, if the modeled sequences display any dependencies between positional identities. In some instances, these dependencies are crucial in correctly accepting or rejecting other sequences as members of the family. MAVL (multiple alignment variation linker) and StickWRLD provide a web-based method to visually survey the model-training sequences to discover and characterize possible dependencies. Initially introduced for nucleic acid sequences, with MAVL/StickWRLD, it is easy to distinguish typical DNA or RNA structural dependencies in input families, identify mixed populations of distinct subfamilies, or discover novel dependencies that result from binding interactions or other selective pressures [W. Ray (2004) Nucleic Acids Res., 32, W59-W63]. Since the announcement of MAVL/StickWRLD for nucleic acids, one of the most requested new features has been the extension of this visualization method to support protein alignments. We are pleased to report that this extension has been successful, that the basic visualization has been augmented in several ways to enhance protein viewing, and that the results with protein alignments are even more dramatic than with NA alignments. MAVL/StickWRLD can be accessed at http://www.microbial-pathogenesis.org/stickwrld/.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Ray WCdoi
10.1093/nar/gki374keywords:
subject
Has Abstractpub_date
2005-07-01 00:00:00pages
W315-9issue
Web Server issueeissn
0305-1048issn
1362-4962pii
33/suppl_2/W315journal_volume
33pub_type
杂志文章abstract:UNLABELLED:The PubMed® database of biomedical citations allows the retrieval of scientific articles studying the function of chemicals in biology and medicine. Mining millions of available citations to search reported associations between chemicals and topics of interest would require substantial human time. We have im...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku432
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abstract::Human transcription factor IIIC contains a 55 kDa polypeptide which specifically interacts with the Adenovirus 2 VAI gene promoter and which mimics most of the DNA binding properties of the entire factor. The specificity and affinity of this protein:DNA interaction was demonstrated by: (i) Separation of purified fract...
journal_title:Nucleic acids research
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journal_title:Nucleic acids research
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doi:10.1093/nar/14.10.3995
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journal_title:Nucleic acids research
pub_type: 杂志文章
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abstract::The fine structure of the melting curve for the linear colE1 DNA has been obtained. To find the ColE1 DNA regions corresponding to peaks in the melting curve's fine structure, we fixed the melted DNA regions with glyoxal /12/. Electron-microscopic denaturation maps were obtained for nine temperature points within the ...
journal_title:Nucleic acids research
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abstract::Current DNA assembly methods for preparing highly purified linear subassemblies require complex and time-consuming in vitro manipulations that hinder their ability to construct megabase-sized DNAs (e.g. synthetic genomes). We have developed a new method designated 'CasHRA (Cas9-facilitated Homologous Recombination Ass...
journal_title:Nucleic acids research
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abstract::The pol gene of all retroviruses is expressed as a gag-pol fusion protein which is proteolytically processed to produce all viral enzymes. In the human immunodeficiency virus (HIV), the gag and pol genes overlap by 241 nucleotides with pol in the -1 phase with respect to gag. The gag-pol fusion is produced via a -1 ri...
journal_title:Nucleic acids research
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abstract::The molecular basis for the DNA binding specificity of the thyroid transcription factor 1 homeodomain (TTF-1HD) has been investigated. Methylation and ethylation interference experiments show that the TTF-1HD alone recapitulates the DNA binding properties of the entire protein. Studies carried out with mutant derivati...
journal_title:Nucleic acids research
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abstract::Eukaryotic cellular mRNAs contain a cap at their 5'-ends, but some viral and cellular mRNAs bypass the cap-dependent mechanism of translation initiation in favor of internal entry of ribosomes at specific RNA sequences. Cap-dependent initiation requires intact initiation factor eIF4G (formerly eIF-4gamma, eIF-4Fgamma ...
journal_title:Nucleic acids research
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abstract::Reversible methylation of the N6 or N1 position of adenine in RNA has recently been shown to play significant roles in regulating the functions of RNA. RNA can also be alkylated upon exposure to endogenous and exogenous alkylating agents. Here we examined how regio-specific methylation at the hydrogen bonding edge of ...
journal_title:Nucleic acids research
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更新日期:2017-09-06 00:00:00
abstract::The Saccharomyces cerevisiae kinase/adenosine triphosphatase Rio1 regulates rDNA transcription and segregation, pre-rRNA processing and small ribosomal subunit maturation. Other roles are unknown. When overexpressed, human ortholog RIOK1 drives tumor growth and metastasis. Likewise, RIOK1 promotes 40S ribosomal subuni...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky618
更新日期:2018-09-06 00:00:00
abstract::Transcription factor (TF) and microRNA (miRNA) are two crucial trans-regulatory factors that coordinately control gene expression. Understanding the impacts of these two factors on the rate of protein sequence evolution is of great importance in evolutionary biology. While many biological factors associated with evolu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt349
更新日期:2013-07-01 00:00:00
abstract::Synchronous plasmodia of Physarum polycephalum in DNA synthesis were pulse-labelled with [oH]- thymidine for time periods of 15 seconds up to 9 minutes, or given a 30 seconds pulse followed by chase periods of 9 minutes up to 6 hours. Sedimentation analysis in alkaline sucrose gradients revealed at least five species ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/2.8.1381
更新日期:1975-08-01 00:00:00
abstract::We describe a rapid fluorescence indicator displacement assay (R-FID) to evaluate the affinity and the selectivity of compounds binding to different DNA structures. We validated the assay using a library of 30 well-known nucleic acid binders containing a variety chemical scaffolds. We used a combination of principal c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky019
更新日期:2018-04-20 00:00:00
abstract::Single nucleotide polymorphisms (SNPs) are, together with copy number variation, the primary source of variation in the human genome. SNPs are associated with altered response to drug treatment, susceptibility to disease and other phenotypic variation. Furthermore, during genetic screens for disease-associated mutatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm979
更新日期:2008-01-01 00:00:00
abstract::The mRNA encoding repressor cI of phage lambda is the only known E. coli message which starts directly with the initiation AUG codon. The ability of in vitro synthesized cI mRNA fragments (150 or 400 nts) to form ternary initiation complexes has been studied using the toeprint method. In the presence of tRNA(Met)f, th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.3.563
更新日期:1992-02-11 00:00:00
abstract::T-region transfer from wild-type Agrobacterium strains is thought to be an orientated process, starting at the right border repeat and terminating at the left border repeat of the T-region. Here we demonstrate that a right border repeat in the inverted orientation relative to the onc-genes can also mediate transfer of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.21.10225
更新日期:1988-11-11 00:00:00
abstract::The persistence of fetal hemoglobin in many patients with deletion type beta thalassemias and the expression patterns of human globin genes in transgenic mice suggest that gamma- to beta-globin gene switching results primarily from competition of gamma- and beta-globin genes for interaction with the beta-globin locus ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.14.2736
更新日期:2000-07-15 00:00:00
abstract::Regulatory T-cells (Treg) play an essential role in the negative regulation of immune answers by developing an attenuated cytokine response that allows suppressing proliferation and effector function of T-cells (CD4(+) Th). The transcription factor FoxP3 is responsible for the regulation of many genes involved in the ...
journal_title:Nucleic acids research
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doi:10.1093/nar/gkr444
更新日期:2011-10-01 00:00:00
abstract::TERC is an RNA component of telomerase. However, TERC is also ubiquitously expressed in most human terminally differentiated cells, which don't have telomerase activity. The function of TERC in these cells is largely unknown. Here, we report that TERC enhances the expression and secretion of inflammatory cytokines by ...
journal_title:Nucleic acids research
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更新日期:2019-09-05 00:00:00
abstract::High-throughput sequencing of 16S rRNA gene amplicons (16S-seq) has become a widely deployed method for profiling complex microbial communities but technical pitfalls related to data reliability and quantification remain to be fully addressed. In this work, we have developed and implemented a set of synthetic 16S rRNA...
journal_title:Nucleic acids research
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更新日期:2017-02-28 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章,评审
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更新日期:2012-07-01 00:00:00
abstract::KU is a heterodimer, consisting of approximately 70 and approximately 80 kDa subunits (KU70 and KU80, respectively), which is involved in a variety of nuclear functions. We generated tbKU80-deficient trypanosomes to explore the potential role of the tbKU complex in telomere maintenance and transcriptional regulation o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh991
更新日期:2004-12-15 00:00:00
abstract::Overexpressed in colon carcinoma-1 (OCC-1) is one of the earliest annotated long noncoding RNAs (lncRNAs) in colorectal cancer (CRC); however, its function remains largely unknown. Here, we revealed that OCC-1 plays a tumor suppressive role in CRC. OCC-1 knockdown by RNA interference promotes cell growth both in vitro...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky214
更新日期:2018-06-20 00:00:00
abstract::Microarrays are an effective tool for monitoring genome-wide gene expression levels. In current microarray analyses, the majority of genes on arrays are frequently eliminated for further analysis because the changes in their expression levels (ratios) are considered to be not significant. This strategy risks failure t...
journal_title:Nucleic acids research
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更新日期:2006-03-14 00:00:00
abstract::Many genetic manipulations are limited by difficulty in obtaining adequate levels of protein expression. Bioinformatic and experimental studies have identified nucleotide sequence features that may increase expression, however it is difficult to assess the relative influence of these features. Zebrafish embryos are ra...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2015-04-20 00:00:00
abstract::We report the first isolation and characterisation of a human Ig V lambda gene. The gene was isolated from a recombinant phage library of human chromosome 22 using a mouse Ig lambda cDNA as probe. DNA sequence analysis predicts a short leader peptide interrupted by an intron of 88 nucleotides, and a mature polypeptide...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.17.6647
更新日期:1984-09-11 00:00:00
abstract::The interactions of self-complementary oligonucleotides with a group of metal-mediated DNA-binding drugs, including chromomycin A(3), mithramycin and the novel compound UK-1, were examined via electrospray ionization quadrupole ion trap mass spectrometry. Both chromomycin and mithramycin were shown to bind preferentia...
journal_title:Nucleic acids research
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更新日期:2001-11-01 00:00:00
abstract::This laboratory has established in previous studies that Pmel 17, a gene expressed specifically in melanocytes, maps near the silver coat color locus (si/si) on mouse chromosome 10. In the current study, we have focused on determining whether or not the si allele carries a mutation in Pmel 17. Pmel 17 cDNA clones, iso...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:1995-01-11 00:00:00
abstract::The "ovalbumin Y" gene, one of three which constitute the ovalbumin gene family in chicken has been completely sequenced. The exact location of exons can be derived from the comparison with the ovalbumin gene sequence and from the map previously established by electron microscopy analysis. During evolution of the Y ge...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.14.4363
更新日期:1982-07-24 00:00:00