Abstract:
:We have developed a novel method for estimating the parameters of hidden Markov models for gene finding in newly sequenced species. Our approach does not rely on curated training data sets, but instead uses extrinsic evidence (including paired-end ditags that have not been used in gene finding previously) and iterative training. This new method is particularly suitable for annotation of species with large evolutionary distance to the closest annotated species. We have used our approach to produce an initial annotation of more than 16,000 genes in the newly sequenced Schistosoma japonicum draft genome. We established the high quality of our predictions by comparison to full-length cDNAs (withdrawn from the extrinsic evidence) and to CEGMA core genes. We also evaluated the effectiveness of the new training procedure on Caenorhabditis elegans genome. ExonHunter and the newest parametric files for S. japonicum genome are available for download at www.bioinformatics.uwaterloo.ca/downloads/exonhunter.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Brejová B,Vinar T,Chen Y,Wang S,Zhao G,Brown DG,Li M,Zhou Ydoi
10.1093/nar/gkp052subject
Has Abstractpub_date
2009-04-01 00:00:00pages
e52issue
7eissn
0305-1048issn
1362-4962pii
gkp052journal_volume
37pub_type
杂志文章abstract::BsoFI , ItaI and Fsp4HI are isoshizomers of Fnu4HI (5'-GC NGC-3'). Both Fnu4HI and BsoFI have previously been shown to be inhibited by cytosine-specific methylation within the recognition sequence. Fnu4HI is inhibited if either the internal cytosine at position 2 or the external cytosine at position 5 of the restricti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.16.3196
更新日期:1997-08-15 00:00:00
abstract::The DNA sequence of a 354 basepair EcoRI-HindIII fragment of plasmid pMB9 which has originally been derived from plasmid pSC101 has been resolved. This fragment contains a promoter for transcription directed towards the EcoRI site. Escherichia coli RNA polymerase binds to a region within the EcoRI-HindIII fragment whi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.7.1535
更新日期:1980-04-11 00:00:00
abstract::Using two primers corresponding to helix 1 and helix 3 regions in the homeodomain, we subjected genomic DNA from Caenorhabditis elegans to amplification by the polymerase chain reaction. Sequence analysis of the amplified products revealed a new homeobox-containing gene, designated ceh-19. This gene was located betwee...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.12.2967
更新日期:1992-06-25 00:00:00
abstract::The Mouse Genome Database (MGD, http://www.informatics.jax.org) is the international community resource for integrated genetic, genomic and biological data about the laboratory mouse. Data in MGD are obtained through loads from major data providers and experimental consortia, electronic submissions from laboratories a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr974
更新日期:2012-01-01 00:00:00
abstract::We report the latest release (version 3.0) of the CATH protein domain database (http://www.cathdb.info). There has been a 20% increase in the number of structural domains classified in CATH, up to 86 151 domains. Release 3.0 comprises 1110 fold groups and 2147 homologous superfamilies. To cope with the increases in di...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl959
更新日期:2007-01-01 00:00:00
abstract::Three peaks of methyltransferase activity specific for MNNG alkylated DNA have been identified from extracts of chemically adapted M. luteus. They are designated as TI to TIII in order to their elution from a Sephadex G-75 column. The first one of these peaks has been purified to homogeneity. TI, is an inducible, unus...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.22.9471
更新日期:1987-11-25 00:00:00
abstract::Much effort has long been devoted to unraveling the coordinated cellular response to genotoxic insults. In view of the difficulty of obtaining human biological samples of homogeneous origin, I have established a set of stable human clones where one DNA repair gene has been stably silenced by means of RNA interference....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm195
更新日期:2007-01-01 00:00:00
abstract::How DNA sequence variation influences gene expression remains poorly understood. Diploid organisms have two homologous copies of their DNA sequence in the same nucleus, providing a rich source of information about how genetic variation affects a wealth of biochemical processes. However, few computational methods have ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz176
更新日期:2019-06-20 00:00:00
abstract::Owing to their great potentials in genetic code extension and the development of nucleic acid-based functional nanodevices, DNA duplexes containing HgII-mediated base pairs have been extensively studied during the past 60 years. However, structural basis underlying these base pairs remains poorly understood. Herein, w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1296
更新日期:2017-03-17 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks671
更新日期:2012-10-01 00:00:00
abstract::To investigate the principles driving recognition between proteins and DNA, we analyzed more than thousand crystal structures of protein/DNA complexes. We classified protein and DNA conformations by structural alphabets, protein blocks [de Brevern, Etchebest and Hazout (2000) (Bayesian probabilistic approach for predi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1273
更新日期:2014-03-01 00:00:00
abstract::A theoretical approach for linkage mapping the genome of any higher eukaryote is described. It uses the polymerase chain reaction, oligonucleotides of random sequence and single haploid cells. Markers are defined and then the DNA of a single sperm is broken at random (eg by gamma-rays) and physically split into 3 aliq...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.17.6795
更新日期:1989-09-12 00:00:00
abstract::Intestinal apolipoprotein B mRNA is edited at nucleotide 6666 by a C to U transition resulting in a translational stop codon. The enzymatic properties of the editing activity were characterised in vitro using rat enterocyte cytosolic extract. The editing activity has no nucleotide or ion cofactor requirement. It shows...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.13.3569
更新日期:1991-07-11 00:00:00
abstract::The rat alpha- and bovine alpha s1-casein genes have been isolated and their 5' sequences determined. The rat alpha-, beta-, gamma- and bovine alpha s1-casein genes contain similar 5' exon arrangements in which the 5' noncoding, signal peptide and casein kinase phosphorylation sequences are each encoded by separate ex...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.4.1883
更新日期:1986-02-25 00:00:00
abstract::It has been shown that the monomethylated cap structure plays important roles in pre-mRNA splicing and nuclear export of RNA. As a candidate for the factor involved in these nuclear events we have previously purified an 80 kDa nuclear cap binding protein (NCBP) from a HeLa cell nuclear extract and isolated its full-le...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.18.3638
更新日期:1995-09-25 00:00:00
abstract::Transcription factor IIIA (TFIIIA) and p43 zinc finger protein form distinct complexes with 5S ribosomal RNA in Xenopus oocytes. Additionally, TFIIIA binds the internal promoter of the 5S RNA gene and supports assembly of a transcription initiation complex. Both proteins have nine tandemly repeated zinc fingers with a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.3.703
更新日期:1998-02-01 00:00:00
abstract::The solution structures of two 27 nt RNA hairpins and their complexes with cobalt(III)-hexammine [Co(NH(3))(6)(3+)] were determined by NMR spectroscopy. The RNA hairpins are variants of the P4 region from Escherichia coli RNase P RNA: a U-to-A mutant changing the identity of the bulged nucleotide, and a U-to-C, C-to-U...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh961
更新日期:2004-12-02 00:00:00
abstract::Therapeutic oligonucleotides are often modified using the phosphorothioate (PS) backbone modification which enhances stability from nuclease mediated degradation. However, substituting oxygen in the phosphodiester backbone with sulfur introduce chirality into the backbone such that a full PS 16-mer oligonucleotide is ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa031
更新日期:2020-02-28 00:00:00
abstract::High-throughput chromosome conformation capture (3C) technologies, such as Hi-C, have made it possible to survey 3D genome structure. However, obtaining 3D profiles at kilobase resolution at low cost remains a major challenge. Therefore, we herein present an algorithm for precise identification of chromatin interactio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx885
更新日期:2017-12-15 00:00:00
abstract::Nuclear actin-related proteins (Arps) are subunits of several chromatin remodelers, but their molecular functions within these complexes are unclear. We report the crystal structure of the INO80 complex subunit Arp8 in its ATP-bound form. Human Arp8 has several insertions in the conserved actin fold that explain its i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks842
更新日期:2012-11-01 00:00:00
abstract::The genes encoding the RNA subunit of ribonuclease P from the unicellular cyanobacterium Synechocystis sp. PCC 6803, and from the heterocyst-forming strains Anabaena sp. PCC 7120 and Calothrix sp. PCC 7601 were cloned using the homologous gene from Anacystis nidulans (Synechococcus sp. PCC 6301) as a probe. The genes ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.23.6331
更新日期:1992-12-11 00:00:00
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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::The petunia rbcS gene SSU301 was introduced into tobacco using Agrobacterium tumefaciens-mediated transformation. The time at which rbcS expression was maximal after transfer of the tobacco plants to the greenhouse was determined. The expression level of the SSU301 gene varied up to 9 fold between individual tobacco p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.19.9267
更新日期:1988-10-11 00:00:00
abstract::IL-2 gene expression in activated T-cells is initiated by chromatin remodeling at the IL-2 proximal promoter and conversion of a transcriptional repressor into a potent transcriptional activator. A purine-box regulator complex was purified from activated Jurkat T-cell nuclei based on sequence-specific DNA binding to t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm117
更新日期:2007-01-01 00:00:00
abstract::Structural domains are considered as the basic units of protein folding, evolution, function and design. Automatic decomposition of protein structures into structural domains, though after many years of investigation, remains a challenging and unsolved problem. Manual inspection still plays a key role in domain decomp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg189
更新日期:2003-02-01 00:00:00
abstract::PUF proteins, named for Drosophila Pumilio (PUM) and Caenorhabditis elegans fem-3-binding factor (FBF), recognize specific sequences in the mRNAs they bind and control. RNA binding by classical PUF proteins is mediated by a characteristic PUM homology domain (PUM-HD). The Puf1 and Puf2 proteins possess a distinct arch...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz583
更新日期:2019-09-19 00:00:00
abstract::Anti-silencing function 1 (Asf1) and Chromatin Assembly Factor 1 (CAF-1) chaperone histones H3/H4 during the assembly of nucleosomes on newly replicated DNA. To understand the mechanism of histone H3/H4 transfer among Asf1, CAF-1 and DNA from a thermodynamic perspective, we developed and employed biophysical approache...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks906
更新日期:2012-12-01 00:00:00
abstract::The B-subunits associated with the replicative DNA polymerases are conserved from Archaea to humans, whereas the corresponding catalytic subunits are not related. The latter belong to the B and D DNA polymerase families in eukaryotes and archaea, respectively. Sequence analysis places the B-subunits within the calcine...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh558
更新日期:2004-04-30 00:00:00
abstract::Many interacting proteins regulate and/or assist the activities of RAD51, a recombinase which plays a critical role in both DNA repair and meiotic recombination. Yeast two-hybrid screening of a human testis cDNA library revealed a new protein, RAD51AP2 (RAD51 Associated Protein 2), that interacts strongly with RAD51. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl665
更新日期:2006-01-01 00:00:00
abstract::Ribosomes transit between two conformational states, non-rotated and rotated, through the elongation cycle. Here, we present evidence that an internal loop in the essential yeast ribosomal protein rpL10 is a central controller of this process. Mutations in this loop promote opposing effects on the natural equilibrium ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1107
更新日期:2014-02-01 00:00:00