Splicing

There are links that deal with the splicing of gene sequences in this section.

Found 19 links

Displaying 15 links

AltAnalyzeTool Content

http://www.altanalyze.org

AltAnalyze is a comprehensive tool for the analysis of gene expression and alternative splicing data from RNA-seq and Affymetrix (exon, gene, junction) datasets at the level of proteins, domains, microRNA binding sites and pathways. The Cytoscape plugin DomainGraph (www.domaingraph.de) allows for visualization of AltAnalyze results at multiple levels of abstraction (e.g., isoform, exon, protein, domain, molecular interactions).

This content is being maintained by NathanSalomonis.

Alternative Splicing Database (ASD) ProjectDatabase Content

http://www.ebi.ac.uk/asd/

Access to the AltSplice, AltExtron and AEdb databases.

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Alternative Splicing GalleryDatabase Content

http://statgen.ncsu.edu/asg/

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.

ASePCRTool Content

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

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.

ASmodelerTool Content

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

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.

ASPicTool Content

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

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.

AStalavistaTool Content

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

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

ESEfinderTool Content

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

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

GeneSplicerTool Content

http://cbcb.umd.edu/software/GeneSplicer/

A fast, flexible system for detecting splice sites in the genomic DNA of various eukaryotes. The system has been trained and tested successfully on Plasmodium falciparum (malaria), Arabidopsis thaliana, human, Drosophila, and rice.

ProSplicerDatabase Content

http://bioinfo.csie.ncu.edu.tw/ProSplicer/

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.

QGRS MapperTool Content

http://bioinformatics.ramapo.edu/QGRS/index.php

Quadruplex forming G-Rich Sequences (QGRS) Mapper searches nucleotide sequences for the presence of G-quartet motifs. QGRS Mapper allows you to view the distribution and composition of QGRS in the context of alternatively spliced isoforms of your gene.

RegRNATool Content

http://regrna.mbc.nctu.edu.tw/

Regulatory RNA (RegRNA) is a server for identifying regulatory RNA motifs and elements in mRNA sequences including: motifs located in the 5\'-UTR and 3\'-UTR; motifs involved in mRNA splicing and transcriptional regulation; other motifs in mRNA such as riboswitches and splice donor/acceptor sites; RNA structural features; and miRNA target sites.

Tags associated with subcategory 'Expression/Splicing'

humans alternative splicing animals messenger rna exons rna splice sites sequence alignment dna sequence analysis genetic databases rna sequence analysis mice computational biology algorithms expressed sequence tags human genome genome introns base sequence molecular sequence data proteins heterogeneous-nuclear ribonucleoproteins zebrafish gene expression profiling genomics benchmarking oligonucleotides tetraodontiformes vldl lipoproteins stochastic processes triglycerides consensus sequence hypoxanthine phosphoribosyltransferase ribonucleic acid regulatory sequences point mutation nucleic acid regulatory sequences statistical models software validation molecular computers reproducibility of results plant rna plant dna neural networks (computer) rna precursors rna splicing genes factual databases dna arabidopsis luminescent proteins nucleic acid databases middle aged software design protein isoforms molecular models artificial intelligence expert systems genetic transcription green fluorescent proteins genetic models forecasting male markov chains gene expression g-quadruplexes drosophila melanogaster automated pattern recognition classification complementary dna genetic linkage transcription factors single nucleotide polymorphism prostatic neoplasms genome-wide association study micrornas binding sites whole transcriptome shotgun sequencing female deoxycholic acid cholic acids adult bile acids and salts antineoplastic antimetabolites colorectal neoplasms RNAseq tumor cell line rna-seq next-generation sequencing fluorouracil neoplasm drug resistance reverse transcriptase polymerase chain reaction chromosomes tissue distribution neoplasm proteins genetic predisposition to disease plant proteins plants protein sequence analysis rats plant genome ldl lipoproteins hyperlipidemias