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Links tagged with 'messenger rna'

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Found 52 links

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ASePCRTool Content

http://genome.ewha.ac.kr/ASePCR/

DNA > Tools For the Bench
Expression > Splicing

ASePCR (Alternative Splicing electronic PCR) is a tool for carrying out e-PCR to detect differences in amplicon sizes in transcripts from different tissues and organs.

NAR Web Server Issue 2005
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tagsalgorithms alternative splicing animals base sequence expressed sequence tags humans messenger rna mice molecular sequence data rats reverse transcriptase polymerase chain reaction tissue distribution

AsiDesignerTool Content

http://sysbio.kribb.re.kr/AsiDesigner/

RNA > Structure Prediction, Visualization, and Design

AsiDesigner is a design software system for siRNA design, that takes into account alternative splicing for mRNA level gene silencing. The software also has the capacity to design siRNAs for silencing of multiple mRNAs simultaneously, to score the performance of designed siRNAs, to search for off-targets with BLAST and FASTA algorithms, and to check for secondary structure energy of siRNAs.

NAR Web Server Issue 2008
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tagsalgorithms alternative splicing messenger rna rna interference rna sequence analysis small interfering rna

ASmodelerTool Content

http://genome.ewha.ac.kr/ECgene/ASmodeler/

Expression > Splicing
Model Organisms > Mouse and Rat
Sequence Comparison > Analysis of Aligned Sequences

Gene modeling server which focuses on the modeling of alternative splicing. It is based on the alignment of mRNA, EST and protein sequences and combines genome-based clustering and transcript assembly. Supports human, mouse and rat genomes.

NAR Web Server Issue 2004
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tagsalgorithms alternative splicing animals exons expressed sequence tags genetic models genome humans messenger rna mice molecular sequence data protein sequence analysis rats rna sequence analysis sequence alignment

ASPicTool Content

http://t.caspur.it/ASPIC/

Expression > Splicing
Expression > cDNA, EST, SAGE
Sequence Comparison > Other Alignment Tools

Alternative Splicing Prediction (ASPic) can predict alternative splicing of user submitted genes based on comparative analysis of available transcript and genome data from a variety of species. Results include graphical and tabular views of the splicing patterns of full-length mRNA isoforms compatible with the detected splice sites of the genes as well as structural and functional annotations.

NAR Web Server Issue 2006
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tagsalgorithms alternative splicing animals base sequence benchmarking exons gene expression profiling genomics heterogeneous-nuclear ribonucleoproteins humans introns messenger rna molecular computers molecular models protein isoforms rna splice sites sequence alignment software design software validation

ASPicDBDatabase Content

http://www.caspur.it/ASPicDB/

Human Genome > Databases
Protein > Databases

ASPicDB provides a unique annotation resource of human protein variants generated by alternative splicing. A total of 256,939 protein variants from 17,191 multi-exon genes have been extensively annotated through machine learning tools providing information of the protein type (globular and transmembrane), localization, presence of PFAM domains, signal peptides, GPI-anchor propeptides, transmembrane and coiled-coil segments. Furthermore, full-length variants can be now specifically selected based on the annotation of CAGE-tags and polyA signal and/or polyA sites, marking transcription initiation and termination sites, respectively. The retrieval can be carried out at gene, transcript, exon, protein or splice site level allowing the selection of data sets fulfilling one or more features settled by the user.

This content is being maintained by Graziano Pesole.

NAR Database Issue 2011
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tagsalternative splicing exons genetic databases genetic variation humans messenger rna protein isoforms protein sequence analysis proteins

AStalavistaTool Content

http://genome.imim.es/astalavista/

Expression > Splicing

AStalavista (alternative splicing transcriptional landscape visualization tool) dynamically identifies, extracts, and displays alternative splicing events from whole genome annotations and user provided gene sets.

NAR Web Server Issue 2007
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tagsalternative splicing chromosome mapping computational biology dna probes dna sequence analysis genetic databases genome humans messenger rna oligonucleotide array sequence analysis rna splice sites

CARNACTool Content

http://bioinfo.lifl.fr/carnac

RNA > Structure Prediction, Visualization, and Design

Server which predicts conserved secondary structure elements of homologous RNAs. The input of a set of RNA sequences are not required to be previously aligned.

NAR Web Server Issue 2004
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tagsalgorithms catalytic rna cytochromes endoribonucleases enterovirus genetic models messenger rna molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid sequence homology ribonuclease p ribosomal rna rna rna sequence analysis sequence alignment statistical models telomerase viral rna

CLIPZDatabase Content

http://www.clipz.unibas.ch

RNA > Databases

CLIPZ supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other type of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. The CLIPZ platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets.

This content is being maintained by nonb@nih.gov.

NAR Database Issue 2011
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tagsanimals binding sites genetic databases genome humans messenger rna mice rna sequence analysis rna-binding proteins transfer rna untranslated rna

CPCTool Content

http://cpc.cbi.pku.edu.cn/programs/run_cpc.jsp

DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
RNA > Functional RNAs

CPC (Coding Potential Calculator) distinguishes protein-coding from non-coding RNAs based on the sequence features of the input transcripts.

NAR Web Server Issue 2007
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tagsanimals computational biology expressed sequence tags genetic code genetic transcription genetic variation genetic vectors messenger rna mice molecular sequence data nucleic acid databases protein biosynthesis proteins reproducibility of results rna

CytoscapeTool Content

http://www.cytoscape.org/

Protein > Interactions, Pathways, Enzymes

Cytoscape is a visualization platform for use with molecular interaction networks. Interaction data can be integrated with other state data such as gene expression profiles. The input to Cytoscape includes lists of interaction pairs, and tab/space delimited files containing mRNA expression profiles. The nodes of the interaction networks can be filtered by such variables as GO annotations and number of interactions.

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tagsalgorithms archaeal proteins bacteriophage lambda biological models computational biology data mining gene expression profiling gene regulatory networks genomics halobacterium messenger rna neural networks (computer) phenotype protein interaction mapping proteins proteomics software design stochastic processes

DIANA-microTTool Content

http://www.microrna.gr/microT

Expression > Gene Regulation
Human Genome > Genomics
Model Organisms > Fly
Model Organisms > Worm
RNA > Functional RNAs

The DIANA-microT web server predicts targets for miRNAs and provides functional information on the predicted miRNA:target gene interaction from various online biological resources. Updates enable the association of miRNAs to diseases through bibliographic analysis and connection to the UCSC genome browser.

NAR Web Server Issue 2009NAR Web Server Issue 2011
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tagsalgorithms binding sites gene expression regulation messenger rna micrornas rna sequence analysis

ESEfinderTool Content

http://rulai.cshl.edu/tools/ESE/

Expression > Splicing

ESEfinder is a web-based resource for identifing putative ESEs (exonic splicing enhancers), cis-acting motifs responsible for enhancing splicing.

NAR Web Server Issue 2003
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tagsbase sequence consensus sequence exons genetic enhancer elements humans messenger rna point mutation rna precursors rna sequence analysis rna splicing rna-binding proteins

Freiburg RNA ToolsTool Content

http://rna.informatik.uni-freiburg.de

RNA > Functional RNAs
RNA > General Resources
RNA > Motifs
Sequence Comparison > Multiple Sequence Alignments

The Freiburg RNA Tools web server contains tools for the advanced analysis of RNA. The tools IntaRNA, ExpaRNA and LocARNA support the prediction of RNA-RNA interaction, exact RNA matching and alignment of RNA, respectively.

NAR Web Server Issue 2010
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tagsmessenger rna nucleic acid conformation rna rna sequence analysis sequence alignment systems integration untranslated rna

g:ProfilerTool Content

http://biit.cs.ut.ee/gprofiler/

DNA > Annotations
DNA > Sequence Polymorphisms
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

g:Profiler is a set of tools for functional annotation of gene lists that includes: g:GOSt, which retrieves the most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs; g:Convert, for conversion between gene or protein names/IDs; g:Orth, for retrieving orthologs; and, g:Sorter, which searches for similar expression profiles. Functional analysis of SNPs and other DNA polymorphisms is also supported, as is enrichment analysis.

NAR Web Server Issue 2007NAR Web Server Issue 2011
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tagsalgorithms animals computational biology dna gene expression profiling genomics humans messenger rna oligonucleotide array sequence analysis statistical data interpretation

H-InvDBDatabase Content

http://www.h-invitational.jp/

Human Genome > Databases

The H-Invitational Database (H-InvDB) is a comprehensive annotation resource of human genes and transcripts. The latest release of H-InvDB (release 6.2) provides the annotation for 219,765 human transcripts in 43,159 human gene clusters based on human full-length cDNAs and mRNAs. H-InvDB now provides several new annotation features, such as mapping of microarray probes, new gene models, relation to known ncRNAs and information from the Glycogene database. H-InvDB also provides useful data mining resources-'Navigation search', 'H-InvDB Enrichment Analysis Tool (HEAT)' and web service APIs.

This content is being maintained by cyamasak.

NAR Database Issue 2010
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tagsalternative splicing complementary dna computational biology genes genetic databases genetic models genetic polymorphism human genome humans messenger rna microsatellite repeats multigene family nucleic acid databases oligonucleotide array sequence analysis open reading frames single nucleotide polymorphism tertiary protein structure