TcSNP: a database of genetic variation in Trypanosoma cruzi.

Abstract:

:The TcSNP database (http://snps.tcruzi.org) integrates information on genetic variation (polymorphisms and mutations) for different stocks, strains and isolates of Trypanosoma cruzi, the causative agent of Chagas disease. The database incorporates sequences (genes from the T. cruzi reference genome, mRNAs, ESTs and genomic sequences); multiple sequence alignments obtained from these sequences; and single-nucleotide polymorphisms and small indels identified by scanning these multiple sequence alignments. Information in TcSNP can be readily interrogated to arrive at gene sets, or SNP sets of interest based on a number of attributes. Sequence similarity searches using BLAST are also supported. This first release of TcSNP contains nearly 170,000 high-confidence candidate SNPs, derived from the analysis of annotated coding sequences. As new sequence data become available, TcSNP will incorporate these data, mapping new candidate SNPs onto the reference genome sequences.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Ackermann AA,Carmona SJ,Agüero F

doi

10.1093/nar/gkn874

subject

Has Abstract

pub_date

2009-01-01 00:00:00

pages

D544-9

issue

Database issue

eissn

0305-1048

issn

1362-4962

pii

gkn874

journal_volume

37

pub_type

杂志文章
  • An NMR and mutational study of the pseudoknot within the gene 32 mRNA of bacteriophage T2: insights into a family of structurally related RNA pseudoknots.

    abstract::NMR methods were used to investigate a series of mutants of the pseudoknot within the gene 32 messenger RNA of bacteriophage T2, for the purpose of investigating the range of sequences, stem and loop lengths that can form a similar pseudoknot structure. This information is of particular relevance since the T2 pseudokn...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/25.6.1130

    authors: Du Z,Hoffman DW

    更新日期:1997-03-15 00:00:00

  • 4'-Acylated thymidine 5'-triphosphates: a tool to increase selectivity towards HIV-1 reverse transcriptase.

    abstract::4'-Acylated thymidines represent a new class of DNA chain terminators, since they have been shown to act as post-incorporation chain-terminating nucleotides despite the presence of a free 3'-hydroxyl group. Here, we describe the action of the 4'-acetyl- (MeTTP) and 4'-propanoylthymidine 5'-triphosphate (EtTTP) on HIV-...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/26.17.4063

    authors: Marx A,Amacker M,Stucki M,Hübscher U,Bickle TA,Giese B

    更新日期:1998-09-01 00:00:00

  • A Protein Classification Benchmark collection for machine learning.

    abstract::Protein classification by machine learning algorithms is now widely used in structural and functional annotation of proteins. The Protein Classification Benchmark collection (http://hydra.icgeb.trieste.it/benchmark) was created in order to provide standard datasets on which the performance of machine learning methods ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl812

    authors: Sonego P,Pacurar M,Dhir S,Kertész-Farkas A,Kocsor A,Gáspári Z,Leunissen JA,Pongor S

    更新日期:2007-01-01 00:00:00

  • Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression.

    abstract::DNA adenine methyltransferase (Dam) is widespread and conserved among the γ-proteobacteria. Methylation of the Ade in GATC sequences regulates diverse bacterial cell functions, including gene expression, mismatch repair and chromosome replication. Dam also controls virulence in many pathogenic Gram-negative bacteria. ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv251

    authors: Horton JR,Zhang X,Blumenthal RM,Cheng X

    更新日期:2015-04-30 00:00:00

  • Theoretical melting profiles and denaturation maps of DNA with known sequence: fdDNA.

    abstract::Differential melting profiles and denaturation maps are calculated for fdDNA whose sequence of nucleotides has been determined recently. The melting profiles for the total DNA and a number of its restriction fragments are compared with experimental data taken from literature. The comparison enables one to correlate a ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/5.7.2547

    authors: Vologodskii AV,Frank-Kamenetskii MD

    更新日期:1978-07-01 00:00:00

  • A switch region inversion contributes to the aberrant rearrangement of a mu immunoglobulin heavy chain gene in MPC-11 cells.

    abstract::We describe the unique features of an aberrantly rearranged mu immunoglobulin heavy chain gene isolated from MPC-11 cells (a gamma 2b producing Balb/c plasmacytoma). A novel rearrangement has occurred 1.5 Kb 5' of the MPC-11 mu gene (denoted 18b mu) resulting in the deletion of the majority of the repetitive switch re...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/10.23.7751

    authors: Greenberg R,Lang RB,Diamond MS,Marcu KB

    更新日期:1982-12-11 00:00:00

  • High efficiency transformation of E. coli by high voltage electroporation.

    abstract::E. coli can be transformed to extremely high efficiencies by subjecting a mixture of cells and DNA to brief but intense electrical fields of exponential decay waveform (electroporation). We have obtained 10(9) to 10(10) transformants/micrograms with strains LE392 and DH5 alpha, and plasmids pUC18 and pBR329. The proce...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/16.13.6127

    authors: Dower WJ,Miller JF,Ragsdale CW

    更新日期:1988-07-11 00:00:00

  • G-quadruplexes as novel cis-elements controlling transcription during embryonic development.

    abstract::G-quadruplexes are dynamic structures folded in G-rich single-stranded DNA regions. These structures have been recognized as a potential nucleic acid based mechanism for regulating multiple cellular processes such as replication, transcription and genomic maintenance. So far, their transcriptional role in vivo during ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw011

    authors: David AP,Margarit E,Domizi P,Banchio C,Armas P,Calcaterra NB

    更新日期:2016-05-19 00:00:00

  • Telomeric circles are abundant in the stn1-M1 mutant that maintains its telomeres through recombination.

    abstract::Some human cancers maintain their telomeres using the alternative lengthening of telomeres (ALT) mechanism; a process thought to involve recombination. Different types of recombinational telomere elongation pathways have been identified in yeasts. In senescing yeast telomerase deletion (ter1-Delta) mutants with very s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp814

    authors: Basenko EY,Cesare AJ,Iyer S,Griffith JD,McEachern MJ

    更新日期:2010-01-01 00:00:00

  • Ligation-independent cloning of PCR products (LIC-PCR).

    abstract::A new procedure has been developed for the efficient cloning of complex PCR mixtures, resulting in libraries exclusively consisting of recombinant clones. Recombinants are generated between PCR products and a PCR-amplified plasmid vector. The procedure does not require the use of restriction enzymes, T4 DNA ligase or ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/18.20.6069

    authors: Aslanidis C,de Jong PJ

    更新日期:1990-10-25 00:00:00

  • Assembly: a resource for assembled genomes at NCBI.

    abstract::The NCBI Assembly database (www.ncbi.nlm.nih.gov/assembly/) provides stable accessioning and data tracking for genome assembly data. The model underlying the database can accommodate a range of assembly structures, including sets of unordered contig or scaffold sequences, bacterial genomes consisting of a single compl...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv1226

    authors: Kitts PA,Church DM,Thibaud-Nissen F,Choi J,Hem V,Sapojnikov V,Smith RG,Tatusova T,Xiang C,Zherikov A,DiCuccio M,Murphy TD,Pruitt KD,Kimchi A

    更新日期:2016-01-04 00:00:00

  • Human microRNA hsa-miR-125a-5p interferes with expression of hepatitis B virus surface antigen.

    abstract::MicroRNAs are small non-coding RNAs that modulate gene expression at post-transcriptional level, playing a crucial role in cell differentiation and development. Recently, some reports have shown that a limited number of mammalian microRNAs are also involved in anti-viral defense. In this study, the analysis of the hep...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkr067

    authors: Potenza N,Papa U,Mosca N,Zerbini F,Nobile V,Russo A

    更新日期:2011-07-01 00:00:00

  • Microfluidic automated plasmid library enrichment for biosynthetic gene cluster discovery.

    abstract::Microbial biosynthetic gene clusters are a valuable source of bioactive molecules. However, because they typically represent a small fraction of genomic material in most metagenomic samples, it remains challenging to deeply sequence them. We present an approach to isolate and sequence gene clusters in metagenomic samp...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa131

    authors: Xu P,Modavi C,Demaree B,Twigg F,Liang B,Sun C,Zhang W,Abate AR

    更新日期:2020-05-07 00:00:00

  • Evolutionarily conserved and non-conserved retrovirus restriction activities of artiodactyl APOBEC3F proteins.

    abstract::The APOBEC3 proteins are unique to mammals. Many inhibit retrovirus infection through a cDNA cytosine deamination mechanism. HIV-1 neutralizes this host defense through Vif, which triggers APOBEC3 ubiquitination and degradation. Here, we report an APOBEC3F-like, double deaminase domain protein from three artiodactyls:...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl721

    authors: Jónsson SR,Haché G,Stenglein MD,Fahrenkrug SC,Andrésdóttir V,Harris RS

    更新日期:2006-01-01 00:00:00

  • Quantitation of supercoiled circular content in plasmid DNA solutions using a fluorescence-based method.

    abstract::A method for quantifying the proportion of supercoiled circular (SC) forms in DNA solutions is described. The method (SCFluo) takes advantage of the reversible denaturation property of SC forms and the high specificity of the PicoGreen fluorochrome for double-stranded (ds)DNA. Fluorescence values of forms capable of r...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/28.12.e57

    authors: Levy MS,Lotfian P,O'Kennedy R,Lo-Yim MY,Shamlou PA

    更新日期:2000-06-15 00:00:00

  • Target specificity of neuronal RNA-binding protein, Mel-N1: direct binding to the 3' untranslated region of its own mRNA.

    abstract::We have identified cDNAs encoding Mel-N1, the mouse homologue of a human nervous system-specific RNA-binding protein, Hel-N1. Two major mRNA transcripts of Mel-N1 were detected predominantly in the adult mouse brain by Northern blot analysis. To gain insight into the RNA binding specificity of Mel-N1, we performed ite...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/24.11.2011

    authors: Abe R,Yamamoto K,Sakamoto H

    更新日期:1996-06-01 00:00:00

  • Quantitation of RNA editing substrates, products and potential intermediates: implications for developmental regulation.

    abstract::Kinetoplast mitochondrial RNA editing is the developmentally regulated post-transcriptional process of uridine insertion and deletion in mRNAs directed by short guide RNAs (gRNAs), which creates functional mRNAs. Two mechanisms are proposed: transesterification which predicts gRNA/mRNA chimeric intermediates, and enzy...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/23.4.708

    authors: Riley GR,Myler PJ,Stuart K

    更新日期:1995-02-25 00:00:00

  • Defects in interstrand cross-link uncoupling do not account for the extreme sensitivity of ERCC1 and XPF cells to cisplatin.

    abstract::The anticancer drug cisplatin reacts with DNA leading to the formation of interstrand and intrastrand cross-links that are the critical cytotoxic lesions. In contrast to cells bearing mutations in other components of the nucleotide excision repair apparatus (XPB, XPD, XPG and CSB), cells defective for the ERCC1-XPF st...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkf479

    authors: De Silva IU,McHugh PJ,Clingen PH,Hartley JA

    更新日期:2002-09-01 00:00:00

  • The p16INK4a tumor suppressor controls p21WAF1 induction in response to ultraviolet light.

    abstract::p16INK4a and p21WAF1, two major cyclin-dependent kinase inhibitors, are the products of two tumor suppressor genes that play important roles in various cellular metabolic pathways. p21WAF1 is up-regulated in response to different DNA damaging agents. While the activation of p21WAF1 is p53-dependent following -rays, th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl1075

    authors: Al-Mohanna MA,Al-Khalaf HH,Al-Yousef N,Aboussekhra A

    更新日期:2007-01-01 00:00:00

  • Hierarchy of nonhomologous end-joining, single-strand annealing and gene conversion at site-directed DNA double-strand breaks.

    abstract::In mammalian cells, DNA double-strand breaks (DSBs) are repaired by three pathways, nonhomologous end-joining (NHEJ), gene conversion (GC) and single-strand annealing (SSA). These pathways are distinct with regard to repair efficiency and mutagenic potential and must be tightly controlled to preserve viability and gen...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn347

    authors: Mansour WY,Schumacher S,Rosskopf R,Rhein T,Schmidt-Petersen F,Gatzemeier F,Haag F,Borgmann K,Willers H,Dahm-Daphi J

    更新日期:2008-07-01 00:00:00

  • A multifunctional expression vector for an anti-HIV-1 ribozyme that produces a 5'- and 3'-trimmed trans-acting ribozyme, targeted against HIV-1 RNA, and cis-acting ribozymes that are designed to bind to and thereby sequester trans-activator proteins such

    abstract::We previously constructed a multiribozyme expression vector by combining cis- and trans-acting ribozymes and we showed that several ribozymes, each directed against a different target in the HIV genome and acting independently in a 'shotgun' manner, markedly increased the efficiency of cleavage of HIV RNA in vitro [Oh...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/22.23.5060

    authors: Yuyama N,Ohkawa J,Koguma T,Shirai M,Taira K

    更新日期:1994-11-25 00:00:00

  • Overlapping promoter targeting by Elk-1 and other divergent ETS-domain transcription factor family members.

    abstract::ETS-domain transcription factors play important roles in controlling gene expression in a variety of different contexts; however, these proteins bind to very similar sites and it is unclear how in vivo specificity is achieved. In silico analysis is unlikely to reveal specific targets for individual family members and ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp804

    authors: Boros J,O'Donnell A,Donaldson IJ,Kasza A,Zeef L,Sharrocks AD

    更新日期:2009-12-01 00:00:00

  • NCBI's LocusLink and RefSeq.

    abstract::The NCBI has introduced two new web resources-LocusLink and RefSeq-that facilitate retrieval of gene-based information and provide reference sequence standards. These resources are designed to provide a non-redundant view of current knowledge about human genes, transcripts and proteins. Additional information about th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/28.1.126

    authors: Maglott DR,Katz KS,Sicotte H,Pruitt KD

    更新日期:2000-01-01 00:00:00

  • Isolation of mouse reticulocyte globin messenger ribonucleoprotein by affinity chromatography using oligo(T)-cellulose.

    abstract::Mouse globin messenger ribonucleoprotein (mRNP) has been isolated from reticulocyte polysomes by affinity chromatography to oligo(T)-cellulose, using a procedure modified from that of Lindberg and Sundquist. The messenger RNA and protein moieties fo the mRNP are indistinguishable from those isolated by less rapid tech...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/2.12.2251

    authors: Burns AT,Williamson R

    更新日期:1975-12-01 00:00:00

  • Isolation and characterization of the activated B-cell factor 1 homolog in Caenorhabditis elegans.

    abstract::Members of the basic helix-loop-helix (bHLH) family of transcription factors regulate a wide array of developmental processes in many cell types, including cell fate specification, differentiation and morphogenesis. Our studies describe the cloning of a gene from the nematode Caenorhabditis elegans that is closely rel...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/29.21.4423

    authors: Nguyen L,Round J,O'Connell R,Geurts P,Funes-Duran M,Wong J,Jongeward G,Vierra CA

    更新日期:2001-11-01 00:00:00

  • Gene delivery by dendrimers operates via a cholesterol dependent pathway.

    abstract::Understanding the cellular uptake and intracellular trafficking of dendrimer-DNA complexes is an important prerequisite for improving the transfection efficiency of non-viral vector-mediated gene delivery. Dendrimers are synthetic polymers used for gene transfer. Although these cationic molecules show promise as versa...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkh595

    authors: Manunta M,Tan PH,Sagoo P,Kashefi K,George AJ

    更新日期:2004-05-17 00:00:00

  • X chromosome inactivation of the human TIMP gene.

    abstract::X chromosome inactivation results in the cis-limited inactivation of most, but not all, genes on one of the two X chromosomes in mammalian females. The molecular basis for inactivation is unknown. In order to examine the transcriptional activity of human X-linked genes, a series of mouse-human somatic cell hybrids und...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/18.14.4191

    authors: Brown CJ,Flenniken AM,Williams BR,Willard HF

    更新日期:1990-07-25 00:00:00

  • Common TFIIH recruitment mechanism in global genome and transcription-coupled repair subpathways.

    abstract::Nucleotide excision repair is initiated by two different damage recognition subpathways, global genome repair (GGR) and transcription-coupled repair (TCR). In GGR, XPC detects DNA lesions and recruits TFIIH via interaction with the pleckstrin homology (PH) domain of TFIIH subunit p62. In TCR, an elongating form of RNA...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx970

    authors: Okuda M,Nakazawa Y,Guo C,Ogi T,Nishimura Y

    更新日期:2017-12-15 00:00:00

  • ST1710-DNA complex crystal structure reveals the DNA binding mechanism of the MarR family of regulators.

    abstract::ST1710, a member of the multiple antibiotic resistance regulator (MarR) family of regulatory proteins in bacteria and archaea, plays important roles in development of antibiotic resistance, a global health problem. Here, we present the crystal structure of ST1710 from Sulfolobus tokodaii strain 7 complexed with salicy...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp496

    authors: Kumarevel T,Tanaka T,Umehara T,Yokoyama S

    更新日期:2009-08-01 00:00:00

  • Site-specific DNA binding of nuclear factor I: effect of the spacer region.

    abstract::Nuclear factor I (NFI) is a site-specific DNA binding protein required for the replication of adenovirus type 2 DNA in vitro and in vivo. To study sequence requirements for the interaction of NFI with DNA, we have measured the binding of the protein to a variety of synthetic sites. Binding sites for NFI (FIB sites) we...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/15.14.5545

    authors: Gronostajski RM

    更新日期:1987-07-24 00:00:00