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Links tagged with 'exons'

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AltAnalyzeTool Content

http://www.altanalyze.org

Expression > Splicing

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.

NAR Web Server Issue 2010
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tagsalternative splicing animals exons gene expression profiling humans mice rats

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

AUGUSTUSTool Content

http://bioinf.uni-greifswald.de/augustus

DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Splicing
Protein > Domains and Motifs

AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface, or downloaded and run locally.

This content is being maintained by Mario Stanke.

NAR Web Server Issue 2004NAR Web Server Issue 2005NAR Web Server Issue 2006
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tagsadult algorithms alternative splicing animals artificial intelligence automated pattern recognition base sequence bile acids and salts cholic acids chromosome mapping computer simulation deoxycholic acid dna sequence analysis drosophila melanogaster exons female gene components gene expression genes genetic databases genetic models genetic variation genomics human genome humans hypercholesterolemia hyperlipidemias introns ldl lipoproteins male markov chains middle aged molecular sequence data proteins sequence alignment statistical models stochastic processes triglycerides vldl lipoproteins

CSTminerTool Content

http://www.caspur.it/CSTminer/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Sequence Comparison > Analysis of Aligned Sequences

CSTminer searches for Conserved Sequence Tags (CST) in pairwise comparisons of genomic sequences. Output is a graphical map showing the location of CSTs overlayed with known Ensembl exons and ESTs. A scoring system reflects coding or non-coding potential of these conserved blocks.

NAR Web Server Issue 2004
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tagsanimals conserved sequence exons genomics humans intergenic dna mice nucleic acid regulatory sequences sequence tagged sites

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

eShadowTool Content

http://eshadow.dcode.org/

Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

A tool for phylogenetic shadowing of multiple sequences from closely related species. This analyses of multiple sequence alignments can be used to predict putative functional elements.

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tagsanimals computational biology conserved sequence exons genetic databases humans intergenic dna papio peptides proteins software design tertiary protein structure

FeatureMap3DTool Content

http://www.cbs.dtu.dk/services/FeatureMap3D/

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Similarity Searching

FeatureMap3D is a tool to map protein features and sequence conservation onto homologous structures in PDB.

NAR Web Server Issue 2006
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tagsamino acid sequence amino acid sequence homology amino acids conserved sequence exons molecular models protein conformation protein databases protein structural homology proteins sequence alignment

FirstEFTool Content

http://rulai.cshl.org/tools/FirstEF/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

First Exon Finder (FirstEF) is a 5\' terminal exon and promoter prediction program. It consists of different discriminant functions structured as a decision tree.

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tagscpg islands exons genetic promoter regions human chromosomes human genome humans

GENSCANTool Content

http://genes.mit.edu/GENSCAN.html

DNA > Gene Prediction

Identification of complete gene structures in genomic DNA.

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tagsanimals dna dna sequence analysis exons genes genetic models genetic promoter regions genetic techniques genetic transcription human genome humans introns markov chains molecular sequence data nucleic acid repetitive sequences probability protein biosynthesis proteins rna splicing vertebrates

IMCB - Fugu Genome ProjectTool Content

http://www.fugu-sg.org/

Model Organisms > Fish

Lots of information on fugu including complete draft sequence, annotations, comparative vertebrate genomics, phylogenies, publications, and information about the fugu genome project; has some very useful tools including annotation tools, an Ensembl mirror, and BLAST.

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tagsanimals base sequence biological evolution computational biology conserved sequence cosmids dna dna sequence analysis dna transposable elements exons factual databases fish proteins fishes gene duplication gene library gene order genetic models genome genomics human genome humans introns japan mammals microsatellite repeats molecular evolution molecular sequence data nucleic acid repetitive sequences open reading frames phylogeny physical chromosome mapping poisonous fishes proteins proteome research satellite dna sequence alignment synteny takifugu vertebrates

MaMTool Content

http://compbio.cs.sfu.ca/MAM.htm

Sequence Comparison > Analysis of Aligned Sequences

The Multiple alignment Manipulator (MaM) takes a multiple alignment of genomic sequences as input and calculates the locations of exons, common repeat elements and unique regions based on user-selected programs/information. The graphical display also allows users to focus an assessment of sequence variation on the identified regions.

NAR Web Server Issue 2005
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tagsexons genomics nucleic acid repetitive sequences phylogeny sequence alignment

MutScreenerTool Content

http://bioinfo.bsd.uchicago.edu/MutScreener.html

DNA > Tools For the Bench

MutScreener is a human-specific primer design tool that considers gene annotation information to design primers for mutation screening. Users can provide custom gene annotation or use existing public gene annotations.

NAR Web Server Issue 2006
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tagsdna primers exons genetic promoter regions genomics human genome humans polymerase chain reaction

NCBI Human DNA Reference SequenceDatabase Content

http://www.ncbi.nlm.nih.gov/RefSeq/

DNA > Sequence Retrieval and Submission
Human Genome > Annotations
Model Organisms > Mouse and Rat
Model Organisms > Yeast

Downloadable human DNA reference sequence as well as other reference genome sequences.

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tagsamino acid sequence animals base sequence dna sequence analysis exons genetic databases genome genomics humans messenger rna mice national library of medicine (u.s.) nucleic acid databases protein databases protein sequence analysis proteins pseudogenes rats reference standards rna sequence analysis sequence analysis systems integration united states untranslated rna