> Tag > Links tagged with 'rna splice sites'

Links tagged with 'rna splice sites'

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Alternative Splicing GalleryDatabase Content

http://statgen.ncsu.edu/asg/ [open in a new window]

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Expression > Splicing

The Alternative Splicing Gallery (ASG) takes an identifier such as an EnsEMBL gene ID or a RefSeq ID as input, and provides a graph mapping splice events to transcript information. The user can also view GO information for the record, and select one or more exons and download the resulting sequence. ASG also links out to other alternative splicing databases like ProSplicer.

links directory index: 90
TitlePublication YearGoogle Scholar Citation Count
The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome200490
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tagsalternative splicing dna sequence analysis genetic transcription human genome humans nucleic acid databases rna sequence analysis rna splice sites sequence alignment

AStalavistaTool Content

http://genome.imim.es/astalavista/ [open in a new window]

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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.

links directory index: 16
TitlePublication YearGoogle Scholar Citation Count
ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets200716
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

DBASS3 and DBASS5Database Content

http://www.dbass.org.uk/ [open in a new window]

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DNA > Databases

DBASS3 and DBASS5 provide comprehensive repositories of new exon boundaries that were induced by pathogenic mutations in human disease genes. Aberrant 5'- and 3'-splice sites were activated either by mutations in the consensus sequences of natural exon-intron junctions (cryptic sites) or elsewhere ('de novo' sites). DBASS3 and DBASS5 data can be searched by disease phenotype, gene, mutation, location of aberrant splice sites in introns and exons and their distance from authentic counterparts, by bibliographic references and by the splice-site strength estimated with several prediction algorithms. The user can also retrieve reference sequences of both aberrant and authentic splice sites with the underlying mutation.

links directory index: 9
TitlePublication YearGoogle Scholar Citation Count
DBASS3 and DBASS5: databases of aberrant 3'- and 5'-splice sites20119
NAR Database Issue 2011
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tagsdisease humans mutation nucleic acid databases rna splice sites terminology as topic

EUGENE'HOMTool Content

http://genopole.toulouse.inra.fr/bioinfo/eugene/EuGeneHom/cgi-bin/EuGeneHom.pl [open in a new window]

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DNA > Annotations
DNA > Gene Prediction
Model Organisms > Plants

EUGENE'HOM is a gene prediction software for eukaryotic organisms based on comparative analysis. The data is currently tuned for plant sequences of up to 400kb.

links directory index: 37
TitlePublication YearGoogle Scholar Citation Count
EUGENE'HOM: A generic similarity-based gene finder using multiple homologous sequences200337
NAR Web Server Issue 2003
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tagsalgorithms complementary dna dna sequence analysis eukaryotic cells genes genome initiator codon nucleic acid sequence homology plant dna rna splice sites

MapSpliceTool Content

http://www.netlab.uky.edu/p/bioinfo/MapSplice [open in a new window]

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Expression > Splicing
RNA > General Resources

MapSplice is an algorithm for mapping RNA-seq data to reference genome for splice junction discovery.

links directory index: 59
TitlePublication YearGoogle Scholar Citation Count
MapSplice: accurate mapping of RNA-seq reads for splice junction discovery201059
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tagsalgorithms alternative splicing breast neoplasms female gene expression profiling humans rna sequence analysis rna splice sites

mGene.webTool Content

http://www.mgene.org/web [open in a new window]

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DNA > Gene Prediction
Human Genome > Genomics
Model Organisms > General Resources

mGene.web is a web server for the genome wide prediction of protein coding genes from eukaryotic DNA sequences based on pre-computed models of gene structures. Users may also compute their own model using their own data.

links directory index: 35
TitlePublication YearGoogle Scholar Citation Count
mGene: accurate SVM-based gene finding with an application to nematode genomes200927
mGene.web: a web service for accurate computational gene finding20098
NAR Web Server Issue 2009
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tagsalgorithms animals artificial intelligence caenorhabditis caenorhabditis elegans computational biology dna sequence analysis genes genomics helminth genes helminth genome proteins reproducibility of results reverse transcriptase polymerase chain reaction rna splice sites transcription initiation site

ProSplicerDatabase Content

http://bioinfo.csie.ncu.edu.tw/ProSplicer/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Splicing

Database which stores alternative splicing information generated from EST, mRNA and protein alignments with genomic sequence; text-based queries and graphical views of putative splice variants.

links directory index: 38
TitlePublication YearGoogle Scholar Citation Count
ProSplicer: a database of putative alternative splicing information derived from protein, mRNA and expressed sequence tag sequence data200338
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tagsalternative splicing expressed sequence tags genetic databases human genome humans messenger rna proteins rna splice sites sequence alignment

SNPinfoTool Content

http://www.niehs.nih.gov/snpinfo [open in a new window]

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DNA > Sequence Polymorphisms
Expression > Gene Regulation
Expression > Splicing
Protein > 3-D Structure Prediction
RNA > Functional RNAs

A suite of web=based tools for SNP detection. Functional predictions of SNP affect on protein structure, gene regulation, splicing and miRNA binding are incorporated.

links directory index: 60
TitlePublication YearGoogle Scholar Citation Count
SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies200960
NAR Web Server Issue 2009
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tagsbinding sites genes genetic linkage genetic predisposition to disease genome genome-wide association study humans male micrornas prostatic neoplasms reproducibility of results rna splice sites single nucleotide polymorphism systems integration transcription factors

SplicePortTool Content

http://spliceport.cs.umd.edu/ [open in a new window]

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Expression > Splicing

SplicePort makes splice-site predictions for submitted sequences, and allows browsing of the motifs used in the prediction. Feature selection is optimized for human splice sites.

This content is being maintained by rnainfo.

links directory index: 40
TitlePublication YearGoogle Scholar Citation Count
SplicePort--an interactive splice-site analysis tool200740
NAR Web Server Issue 2007
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tagsautomated pattern recognition base sequence chromosome mapping computational biology computer simulation dna dna sequence analysis genetic models genome humans molecular sequence data rna splice sites sequence alignment

SROOGLETool Content

http://sroogle.tau.ac.il [open in a new window]

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Expression > Splicing

SROOGLE is a webserver that makes splicing signal sequence and scoring data available to the biologist in an integrated, visual and user friendly format.

links directory index: 18
TitlePublication YearGoogle Scholar Citation Count
SROOGLE: webserver for integrative, user-friendly visualization of splicing signals200918
NAR Web Server Issue 2009
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tagsexons introns ribonucleic acid regulatory sequences rna splice sites rna splicing systems integration

WebScipio - eukaryotic gene identificationTool Content

http://www.webscipio.org [open in a new window]

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DNA > Gene Prediction
Expression > Splicing
RNA > General Resources
Sequence Comparison > Analysis of Aligned Sequences

Scipio is a tool to determine the precise exon-intron gene structure given a protein sequence and a genome. It identifies splice sites and is able to cope with sequencing errors and genes spanning several contigs. The output contains information about discrepancies that may result from sequencing errors. Scipio has also successfully been used to find homologous genes in related species. WebScipio, allows to search for mutually exclusive spliced exons and tandemly arrayed gene duplicates.

links directory index: 24
TitlePublication YearGoogle Scholar Citation Count
WebScipio: an online tool for the determination of gene structures using protein sequences20089
Scipio: using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species200815
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tagsacetylcholine action potentials algorithms alternative splicing amino acid sequence animals apomorphine atropine base sequence benserazide bromocriptine central nervous system dextroamphetamine diaphragm dna sequence analysis dopamine drosophila melanogaster drosophila proteins epinephrine exon-intron structure exons extrapyramidal tracts female gene duplicates gene prediction gene structure genetic databases genomics haloperidol human parainfluenza virus 3 humans hydroxylamines immunologic deficiency syndromes infant introns kinetics levodopa mathematics molecular sequence data motor activity muscle contraction muscle denervation mutually exclusive splicing nerve degeneration neurological models neuromuscular junction nucleic acid sequence homology oxidation-reduction paramyxoviridae infections physostigmine piribedil planarians protein sequence analysis proteins rats reading frames reserpine rna splice sites sequence alignment software species specificity superoxide dismutase superoxides synaptic transmission tandem gene duplication tetrodotoxin turbellaria user-computer interface viral pneumonia x chromosome

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