Abstract:
:SplicePort is a web-based tool for splice-site analysis that allows the user to make splice-site predictions for submitted sequences. In addition, the user can also browse the rich catalog of features that underlies these predictions, and which we have found capable of providing high classification accuracy on human splice sites. Feature selection is optimized for human splice sites, but the selected features are likely to be predictive for other mammals as well. With our interactive feature browsing and visualization tool, the user can view and explore subsets of features used in splice-site prediction (either the features that account for the classification of a specific input sequence or the complete collection of features). Selected feature sets can be searched, ranked or displayed easily. The user can group features into clusters and frequency plot WebLogos can be generated for each cluster. The user can browse the identified clusters and their contributing elements, looking for new interesting signals, or can validate previously observed signals. The SplicePort web server can be accessed at http://www.cs.umd.edu/projects/SplicePort and http://www.spliceport.org.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Dogan RI,Getoor L,Wilbur WJ,Mount SMdoi
10.1093/nar/gkm407subject
Has Abstractpub_date
2007-07-01 00:00:00pages
W285-91issue
Web Server issueeissn
0305-1048issn
1362-4962pii
gkm407journal_volume
35pub_type
杂志文章abstract::The mouse c-Ki-ras protooncogene promoter contains an unusual DNA element consisting of a 27 bp-long homopurine-homopyrimidine mirror repeat (H-motif) adjacent to a d(C-G)5 repeat. We have previously shown that in vitro these repeats may adopt H and Z conformations, respectively, causing nuclease and chemical hypersen...
journal_title:Nucleic acids research
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doi:10.1093/nar/22.16.3271
更新日期:1994-08-25 00:00:00
abstract::DNA methylation is the best-studied epigenetic modification and describes the conversion of cytosine to 5-methylcytosine. The importance of this phenomenon is that aberrant promoter hypermethylation is a common occurrence in cancer and is frequently associated with gene silencing. Various techniques are currently avai...
journal_title:Nucleic acids research
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更新日期:2006-02-07 00:00:00
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journal_title:Nucleic acids research
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更新日期:2018-07-02 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2015-03-31 00:00:00
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journal_title:Nucleic acids research
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pub_type: 杂志文章
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更新日期:2021-01-25 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
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journal_title:Nucleic acids research
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pub_type: 杂志文章
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pub_type: 杂志文章
doi:10.1093/nar/4.5.1159-a
更新日期:1977-01-01 00:00:00
abstract::Here we employ a set of RNA Polymerase II (Pol II) activity mutants to determine the consequences of increased or decreased Pol II catalysis on gene expression in Saccharomyces cerevisiae. We find that alteration of Pol II catalytic rate, either fast or slow, leads to decreased Pol II occupancy and apparent reduction ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx037
更新日期:2017-05-05 00:00:00
abstract::Alternative splicing of mRNA precursors results in multiple protein variants from a single gene and is critical for diverse cellular processes and development. Xist encodes a long noncoding RNA which is a central player to induce X-chromosome inactivation in female mammals and has two major splicing variants: long and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1227
更新日期:2018-03-16 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.23.4803
更新日期:1997-12-01 00:00:00
abstract::The accurate calculation of protein/nucleic acid-ligand interactions or condensed phase properties by force field-based methods require a precise description of the energetics of intermolecular interactions. Despite the progress made in force fields, small molecule parameterization remains an open problem due to the m...
journal_title:Nucleic acids research
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journal_title:Nucleic acids research
pub_type: 杂志文章
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.14.3364
更新日期:1998-07-15 00:00:00
abstract::Since its conception in 1992, differential display PCR (DD-PCR) has attracted widespread interest. Theoretically an attractive cloning approach, it combines the comparative analysis of several samples with the sensitivity of PCR. Although a large number of studies embracing this technology have been initiated, few nov...
journal_title:Nucleic acids research
pub_type: 杂志文章
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journal_title:Nucleic acids research
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更新日期:1994-12-25 00:00:00
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journal_title:Nucleic acids research
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更新日期:2018-10-12 00:00:00
abstract::TIAR and HuR are mRNA-binding proteins that play important roles in the regulation of translation. They both possess three RNA recognition motifs (RRMs) and bind to AU-rich elements (AREs), with seemingly overlapping specificity. Here we show using SPR that TIAR and HuR bind to both U-rich and AU-rich RNA in the nanom...
journal_title:Nucleic acids research
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journal_title:Nucleic acids research
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更新日期:2012-07-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2012-02-01 00:00:00
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journal_title:Nucleic acids research
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更新日期:2019-11-18 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.15.3307
更新日期:1980-08-11 00:00:00
abstract::A hallmark of defense mechanisms based on clustered regularly interspaced short palindromic repeats (CRISPR) and associated sequences (Cas) are the crRNAs that guide these complexes in the destruction of invading DNA or RNA. Three separate CRISPR-Cas systems exist in the cyanobacterium Synechocystis sp. PCC 6803. Base...
journal_title:Nucleic acids research
pub_type: 杂志文章
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