当前位置： SCI文献检索 > NUCLEIC ACIDS RESEARCH期刊下所有文献 > PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments.

PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments.

Abstract：

:We describe Protogene, a server that can turn a protein multiple sequence alignment into the equivalent alignment of the original gene coding DNA. Protogene relies on a pipeline where every initial protein sequence is BLASTed against RefSeq or NR. The annotation associated with potential matches is used to identify the gene sequence. This gene sequence is then aligned with the query protein using Exonerate in order to extract a coding nucleotide sequence matching the original protein. Protogene can handle protein fragments and will return every CDS coding for a given protein, even if they occur in different genomes. Protogene is available from http://www.tcoffee.org/.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Moretti S,Reinier F,Poirot O,Armougom F,Audic S,Keduas V,Notredame C

doi

10.1093/nar/gkl170

subject

Has Abstract

pub_date

2006-07-01 00:00:00

pages

W600-3

issue

Web Server issue

eissn

0305-1048

issn

1362-4962

pii

34/suppl_2/W600

journal_volume

34

pub_type

杂志文章

相关文献

NUCLEIC ACIDS RESEARCH文献大全
  • FIGfams: yet another set of protein families.

    abstract：:We present FIGfams, a new collection of over 100,000 protein families that are the product of manual curation and close strain comparison. Using the Subsystem approach the manual curation is carried out, ensuring a previously unattained degree of throughput and consistency. FIGfams are based on over 950,000 manually a...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkp698

    authors： Meyer F,Overbeek R,Rodriguez A

    更新日期：2009-11-01 00:00:00

  • A comprehensive framework for prioritizing variants in exome sequencing studies of Mendelian diseases.

    abstract：:Exome sequencing strategy is promising for finding novel mutations of human monogenic disorders. However, pinpointing the casual mutation in a small number of samples is still a big challenge. Here, we propose a three-level filtration and prioritization framework to identify the casual mutation(s) in exome sequencing ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkr1257

    authors： Li MX,Gui HS,Kwan JS,Bao SY,Sham PC

    更新日期：2012-04-01 00:00:00

  • A highly conserved RNA folding region coincident with the Rev response element of primate immunodeficiency viruses.

    abstract：:A series of unusual folding regions (UFR) immediately 3' to the cleavage site of the outer membrane protein (OMP) and transmembrane protein (TMP) were detected in the envelope gene RNA of the human immunodeficiency virus (HIV-1, HIV-2) and simian immunodeficiency virus (SIV) by an extensive Monte Carlo simulation. The...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/18.6.1613

    authors： Le SY,Malim MH,Cullen BR,Maizel JV

    更新日期：1990-03-25 00:00:00

  • HuD binds to three AU-rich sequences in the 3'-UTR of neuroserpin mRNA and promotes the accumulation of neuroserpin mRNA and protein.

    abstract：:Neuroserpin is an axonally secreted serine protease inhibitor expressed in the nervous system that protects neurons from ischemia-induced apoptosis. Mutant neuroserpin forms have been found polymerized in inclusion bodies in a familial autosomal encephalopathy causing dementia, or associated with epilepsy. Regulation ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/30.10.2202

    authors： Cuadrado A,Navarro-Yubero C,Furneaux H,Kinter J,Sonderegger P,Muñoz A

    更新日期：2002-05-15 00:00:00

  • NetVenn: an integrated network analysis web platform for gene lists.

    abstract：:Many lists containing biological identifiers, such as gene lists, have been generated in various genomics projects. Identifying the overlap among gene lists can enable us to understand the similarities and differences between the data sets. Here, we present an interactome network-based web application platform named N...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gku331

    authors： Wang Y,Thilmony R,Gu YQ

    更新日期：2014-07-01 00:00:00

  • Methods to increase reproducibility in differential gene expression via meta-analysis.

    abstract：:Findings from clinical and biological studies are often not reproducible when tested in independent cohorts. Due to the testing of a large number of hypotheses and relatively small sample sizes, results from whole-genome expression studies in particular are often not reproducible. Compared to single-study analysis, ge...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkw797

    authors： Sweeney TE,Haynes WA,Vallania F,Ioannidis JP,Khatri P

    更新日期：2017-01-09 00:00:00

  • Non-specific binding of Na+ and Mg2+ to RNA determined by force spectroscopy methods.

    abstract：:RNA duplex stability depends strongly on ionic conditions, and inside cells RNAs are exposed to both monovalent and multivalent ions. Despite recent advances, we do not have general methods to quantitatively account for the effects of monovalent and multivalent ions on RNA stability, and the thermodynamic parameters f...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gks289

    authors： Bizarro CV,Alemany A,Ritort F

    更新日期：2012-08-01 00:00:00

  • Splicing of constitutive upstream introns is essential for the recognition of intra-exonic suboptimal splice sites in the thrombopoietin gene.

    abstract：:The human thrombopoietin (TPO) gene, which codes for the principal cytokine involved in platelet maturation, shows a peculiar alternative splicing of its last exon, where an intra-exonic 116 nt alternative intron is spliced out in a fraction of its mRNA. To characterize the molecular mechanism underlying this alternat...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/29.4.886

    authors： Romano M,Marcucci R,Baralle FE

    更新日期：2001-02-15 00:00:00

  • Specific fluorescent labeling of 7-(aminomethyl)-7-deazaguanosine located in the anticodon of tRNATyr isolated from E. coli mutant.

    abstract：:Under-modified E. coli tRNATyr that contains 7-(aminomethyl)-7-deazaguanosine in place of Q nucleoside can be chemically modified by dansyl chloride under neutral conditions. Fluorescent labelling specifically occurred only in the 7-(aminomethyl)-7-deazaguanine moiety. The modified tRNATyr was found to be active both ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/7.1.231

    authors： Kasai H,Shindo-Okada N,Noguchi S,Nishimura S

    更新日期：1979-09-11 00:00:00

  • Interaction and effect of annealing temperature on primers used in differential display RT-PCR.

    abstract：:Differential display of mRNA is a simple, sensitive and powerful method to identify differentially expressed gene fragments. The main drawback of differential display is the lack of reproducibility and the inability to read and compare complex gels. This issue results from employing unoptimized primer combinations and...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/26.3.854

    authors： Malhotra K,Foltz L,Mahoney WC,Schueler PA

    更新日期：1998-02-01 00:00:00

  • Double-strand breaks in the myotonic dystrophy type 1 and the fragile X syndrome triplet repeat sequences induce different types of mutations in DNA flanking sequences in Escherichia coli.

    abstract：:The putative role of double-strand breaks (DSBs) created in vitro by restriction enzyme cleavage in or near CGG*CCG or CTG*CAG repeat tracts on their genetic instabilities, both within the repeats and in their flanking sequences, was investigated in an Escherichia coli plasmid system. DSBs at TRS junctions with the ve...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkl612

    authors： Kosmider B,Wells RD

    更新日期：2006-01-01 00:00:00

  • ssDNA diffuses along replication protein A via a reptation mechanism.

    abstract：:Replication protein A (RPA) plays a critical role in all eukaryotic DNA processing involving single-stranded DNA (ssDNA). Contrary to the notion that RPA provides solely inert protection to transiently formed ssDNA, the RPA-ssDNA complex acts as a dynamic DNA processing unit. Here, we studied the diffusion of RPA alon...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkz1202

    authors： Mishra G,Bigman LS,Levy Y

    更新日期：2020-02-28 00:00:00

  • ArrayExpress--a public repository for microarray gene expression data at the EBI.

    abstract：:ArrayExpress is a public repository for microarray data that supports the MIAME (Minimum Information About a Microarray Experiment) requirements and stores well-annotated raw and normalized data. As of November 2004, ArrayExpress contains data from approximately 12,000 hybridizations covering 35 species. Data can be s...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gki056

    authors： Parkinson H,Sarkans U,Shojatalab M,Abeygunawardena N,Contrino S,Coulson R,Farne A,Lara GG,Holloway E,Kapushesky M,Lilja P,Mukherjee G,Oezcimen A,Rayner T,Rocca-Serra P,Sharma A,Sansone S,Brazma A

    更新日期：2005-01-01 00:00:00

  • Site-specific mutagenesis by triple helix-forming oligonucleotides containing a reactive nucleoside analog.

    abstract：:The specific recognition of homopurine-homo pyrimidine regions in duplex DNA by triplex-forming oligonucleotides (TFOs) provides an attractive strategy for genetic manipulation. Alkylation of nucleobases with functionalized TFOs would have the potential for site-directed mutagenesis. Recently, we demonstrated that a T...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gng031

    authors： Nagatsugi F,Sasaki S,Miller PS,Seidman MM

    更新日期：2003-03-15 00:00:00

  • MetaQC: objective quality control and inclusion/exclusion criteria for genomic meta-analysis.

    abstract：:Genomic meta-analysis to combine relevant and homogeneous studies has been widely applied, but the quality control (QC) and objective inclusion/exclusion criteria have been largely overlooked. Currently, the inclusion/exclusion criteria mostly depend on ad-hoc expert opinion or naïve threshold by sample size or platfo...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkr1071

    authors： Kang DD,Sibille E,Kaminski N,Tseng GC

    更新日期：2012-01-01 00:00:00

  • Nuclear origin of specific yeast mitochondrial aminoacyl-tRNA synthetases.

    abstract：:Hydroxylapatite chromatographies of mitochondrial and total enzymes from a rho+ yeast, or from the related rho degrees mitochondrial DNA-less mutant, show the occurrence in the mitochondrial enzyme of one Phe-, one Met-, one Leu-tRNA synthetase peak which elutes distinctly from the cytoplasmic counterpart and charges ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/3.5.1151

    authors： Schneller JM,Schneller C,Martin R,Stahl AJ

    更新日期：1976-05-01 00:00:00

  • The miniF plasmid C protein: sequence, purification and DNA binding.

    abstract：:The C (pifC) protein of miniF represses transcription of its own gene by binding to the pif operator (pifO); it is also needed for replication initiated from the miniF primary origin (ori-1). We have determined the nucleotide sequence of the C gene. The gene has been inserted into an expression vector under Ptrp contr...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/14.24.9699

    authors： Caughey PA,de Feyter R,Lane HE

    更新日期：1986-12-22 00:00:00

  • Identification of an essential proximal sequence element in the promoter of the telomerase RNA gene of Tetrahymena thermophila.

    abstract：:Telomerase is a ribonucleoprotein reverse transcriptase that synthesizes and maintains telomeric DNA. Studies of telomeres and telomerase are facilitated by the large number of linear DNA molecules found in ciliated protozoa, such as Tetrahymena thermophila. To examine the expression of telomerase, we investigated the...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/27.21.4269

    authors： Hargrove BW,Bhattacharyya A,Domitrovich AM,Kapler GM,Kirk K,Shippen DE,Kunkel GR

    更新日期：1999-11-01 00:00:00

  • IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex.

    abstract：:The IMGT/HLA database (http://www.ebi.ac.uk/imgt/hla) has provided a centralized repository for the sequences of the alleles named by the WHO Nomenclature Committee for Factors of the HLA System for the past four years. Since its initial release the database has grown and is the primary source of information for the s...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkg070

    authors： Robinson J,Waller MJ,Parham P,de Groot N,Bontrop R,Kennedy LJ,Stoehr P,Marsh SG

    更新日期：2003-01-01 00:00:00

  • H-DNA and Z-DNA in the mouse c-Ki-ras promoter.

    abstract：:The mouse c-Ki-ras protooncogene promoter contains a homopurine-homopyrimidine domain that exhibits S1 nuclease sensitivity in vitro. We have studied the structure of this DNA region in a supercoiled state using a number of chemical probes for non-B DNA conformations including diethyl pyrocarbonate, osmium tetroxide, ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/19.23.6527

    authors： Pestov DG,Dayn A,Siyanova EYu,George DL,Mirkin SM

    更新日期：1991-12-11 00:00:00

  • LSD 3.0: a comprehensive resource for the leaf senescence research community.

    abstract：:The leaf senescence database (LSD) is a comprehensive resource of senescence-associated genes (SAGs) and their corresponding mutants. Through manual curation and extensive annotation, we updated the LSD to a new version LSD 3.0, which contains 5853 genes and 617 mutants from 68 species. To provide sustainable and reli...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkz898

    authors： Li Z,Zhang Y,Zou D,Zhao Y,Wang HL,Zhang Y,Xia X,Luo J,Guo H,Zhang Z

    更新日期：2020-01-08 00:00:00

  • Studies of the transcription of viral genome in adenovirus 5 transformed cells.

    abstract：:Transcription of the human adenovirus 5 genome in transformed rat embryo cells (DFK3) was investigated using two different approaches. Preferential digestion of transcribed viral sequences by DNase I was analysed using kinetics of renaturation of 32P-labeled Ad5 HpaI restriction fragments in the presence of material w...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/5.1.1

    authors： Frolova EI,Zalmanzon ES,Lukanidin EM,Georgiev GP

    更新日期：1978-01-01 00:00:00

  • Cloning of multiple copies of immunoglobulin variable kappa genes in cosmid vectors.

    abstract：:The possibility of cloning large segments of DNA in cosmid vectors offers distinct advantages, in particular for the study of multigene families. Large size fragments of mouse embryo DNA were successfully cloned in the cosmid pHC 79. Twelve recombinants hybridizing specifically to an immunoglobulin kappa chain variabl...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/9.12.2777

    authors： Cattaneo R,Gorski J,Mach B

    更新日期：1981-06-25 00:00:00

  • Carboxy terminal modifications of the P0 protein reveal alternative mechanisms of nuclear ribosomal stalk assembly.

    abstract：:The P0 scaffold protein of the ribosomal stalk is mainly incorporated into pre-ribosomes in the cytoplasm where it replaces the assembly factor Mrt4. In analyzing the role of the P0 carboxyl terminal domain (CTD) during ribosomal stalk assembly, we found that its complete removal yields a protein that is functionally ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkt637

    authors： Francisco-Velilla R,Remacha M,Ballesta JP

    更新日期：2013-10-01 00:00:00

  • The conformation of adenovirus VAI-RNA in solution.

    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

    authors： Monstein HJ,Philipson L

    更新日期：1981-09-11 00:00:00

  • Identification of the minor guanylated tRNA of rabbit reticulocytes.

    abstract：:Two of the tRNA's found in rabbit reticulocytes are substrates for a post-transcriptional modification leading to the incorporation of guanine into the polynucleotide chain. The major guanylated tRNA was previously identified as tRNA (His). In the present report we show that the minor guanylated tRNA is tRNA (Asn), an...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/3.10.2521

    authors： Farkas WR,Chernoff D

    更新日期：1976-10-01 00:00:00

  • Tetratricopeptide repeat factor XAB2 mediates the end resection step of homologous recombination.

    abstract：:We examined the influence of the tetratricopeptide repeat factor XAB2 on chromosomal break repair, and found that XAB2 promotes end resection that generates the 3' ssDNA intermediate for homologous recombination (HR). Namely, XAB2 is important for chromosomal double-strand break (DSB) repair via two pathways of HR tha...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkw275

    authors： Onyango DO,Howard SM,Neherin K,Yanez DA,Stark JM

    更新日期：2016-07-08 00:00:00

  • The legumin gene family: structure of a B type gene of Vicia faba and a possible legumin gene specific regulatory element.

    abstract：:The field bean, Vicia faba L. var. minor, possesses two sub-families of 11 S legumin genes named A and B. We isolated from a genomic library a B-type gene (LeB4) and determined its primary DNA sequence. Gene LeB4 codes for a 484 amino acid residue prepropolypeptide, encompassing a signal peptide of 22 amino acid resid...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/14.6.2707

    authors： Bäumlein H,Wobus U,Pustell J,Kafatos FC

    更新日期：1986-03-25 00:00:00

  • Diverse transcription influences can be insulated by the Drosophila SF1 chromatin boundary.

    abstract：:Chromatin boundaries regulate gene expression by modulating enhancer-promoter interactions and insulating transcriptional influences from organized chromatin. However, mechanistic distinctions between these two aspects of boundary function are not well understood. Here we show that SF1, a chromatin boundary located in...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkp362

    authors： Majumder P,Roy S,Belozerov VE,Bosu D,Puppali M,Cai HN

    更新日期：2009-07-01 00:00:00

  • Direct quantification of the translocation activities of Saccharomyces cerevisiae Pif1 helicase.

    abstract：:Saccharomyces cerevisiae Pif1 (ScPif1) is known as an ATP-dependent DNA helicase that plays critical roles in a number of important biological processes such as DNA replication, telomere maintenance and genome stability maintenance. Besides its DNA helicase activity, ScPif1 is also known as a single-stranded DNA (ssDN...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkz541

    authors： Lu C,Le S,Chen J,Byrd AK,Rhodes D,Raney KD,Yan J

    更新日期：2019-08-22 00:00:00