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Links tagged with 'introns'

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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

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

DINAMeltTool Content

http://mfold.rna.albany.edu/?q=DINAMelt

DNA > Tools For the Bench
RNA > Structure Prediction, Visualization, and Design

DINAMelt is a tool for predicting hybridization and folding (secondary structure) of DNA and RNA using equilibrium thermodynamic methods.

NAR Web Server Issue 2005
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tagsalgorithms animals bacterial rna base sequence calorimetry dna dna sequence analysis fungal rna genetic hybridization introns molecular sequence data nucleic acid conformation nucleic acid denaturation nucleic acid hybridization oligonucleotides oligoribonucleotides phylogeny rats rna rna sequence analysis single-stranded dna structure-activity relationship temperature theoretical models transition temperature

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

MicroFootPrinterTool Content

http://bio.cs.washington.edu/MicroFootPrinter.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

MicroFootPrinter identifies the conserved motifs in regulatory regions of prokaryotic genomes using the phylogenetic footprinting program FootPrinter.

NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence homology animals archaeal genome bacterial genome computational biology conserved sequence dna footprinting dna sequence analysis fish proteins fos genes genetic promoter regions genomics growth hormone humans insulin interleukin-3 introns metallothionein multigene family myc genes nucleic acid databases nucleic acid regulatory sequences nucleic acid sequence homology phylogeny regulator genes transcriptional regulatory elements

Netgene2Tool Content

http://www.cbs.dtu.dk/services/NetGene2/

Expression > Splicing

The NetGene2 server is a service producing neural network predictions of splice sites in human, C. elegans and A. thaliana DNA.

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tagsalgorithms arabidopsis artificial intelligence exons expert systems factual databases forecasting genetic models green fluorescent proteins introns luminescent proteins molecular sequence data neural networks (computer) plant dna plant rna reproducibility of results rna precursors rna splicing

PLANdbAffyDatabase Content

http://affymetrix2.bioinf.fbb.msu.ru

Expression > Databases

PLANdbAffy contains the results of the alignment of probe sequences from five Affymetrix expression microarrays to the human genome. Probes matching the transcript-coding regions in the correct orientation have been determined. For each such probe alignment region, the mRNA and EST sequences that contain the probe sequence have also been determined. In the textual part of the database interface, data on the sequences that cover the probe alignment region and SNPs that are located inside it is summarized. The graphical part of our database interface is implemented as custom tracks to the UCSC genome browser that allows one to utilize all the data that are offered by UCSC browser.

NAR Database Issue 2010
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tagsalternative splicing computational biology genetic databases genome humans introns nucleic acid databases nucleic acid hybridization oligonucleotide array sequence analysis protein databases sequence alignment single nucleotide polymorphism

Rescue-ESETool Content

http://genes.mit.edu/burgelab/rescue-ese/

DNA > Structure and Sequence Feature Detection
Expression > Splicing

Server for the identification of hexnucleotide exonic splicing enhancers (ESEs). Also contains a list of 238 identified ESEs for human genes.

NAR Web Server Issue 2004
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tagsanimals complementary dna computational biology consensus sequence dna sequence analysis exons genes human genome humans hypoxanthine phosphoribosyltransferase introns messenger rna mice nucleic acid databases nucleic acid regulatory sequences oligonucleotides point mutation ribonucleic acid regulatory sequences rna precursors rna sequence analysis rna splicing tetraodontiformes zebrafish

S. pombe genomeDatabase Content

http://www.sanger.ac.uk/Projects/S_pombe/

Model Organisms > Yeast

Schizosaccharomyces pombe Genome Sequencing Project.

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tagsbase sequence centromere chromosome mapping dna sequence analysis eukaryotic cells fungal chromosomes fungal dna fungal genome fungal proteins gene duplication humans inborn genetic diseases introns schizosaccharomyces tertiary protein structure

SMARTTool Content

http://smart.embl-heidelberg.de/

Protein > Domains and Motifs

SMART (Simple Modular Architecture Research Tool) is a web tool for the identification and annotation of protein domains, and provides a platform for the comparative study of complex domain architectures in genes and proteins.

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tagsalgorithms amino acid sequence animals computational biology genome genomics humans introns molecular sequence data phylogeny protein databases proteins proteome proteomics sequence alignment sequence analysis tertiary protein structure

SROOGLETool Content

http://sroogle.tau.ac.il

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.

NAR Web Server Issue 2009
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tagsexons introns ribonucleic acid regulatory sequences rna splice sites rna splicing systems integration

TIGR Software ToolsResource Content

http://www.tigr.org/software/

DNA > Annotations
DNA > Gene Prediction
DNA > Mapping and Assembly
DNA > Structure and Sequence Feature Detection
Expression > Transcript Expression Analysis
Sequence Comparison > Comparative Genomics

A list of open-source software packages available for free from The Institute for Genomic Research (TIGR).

NAR Web Server Issue 2003
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tagsarabidopsis dna sequence analysis eukaryotic cells exons genes introns markov chains plant genes

tRNAscan-SETool Content

http://lowelab.ucsc.edu/tRNAscan-SE/

RNA > Functional RNAs

tRNAscan-SE allows you to search for tRNA genes in genomic sequence. (site hosted by Lowe Lab at UCSC)

NAR Web Server Issue 2005
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tagsanimals bacterial rna evaluation studies as topic factual databases genome genomics introns rna small nucleolar rna transfer rna

Virtual RibosomeTool Content

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

DNA > DNA and Genomic Analysis
DNA > Gene Prediction

The Virtual Ribosome is a DNA translation tool with a built-in ORF finder that allows the use of alternative start codons, the IUPAC degenerate DNA alphabet, and all translation tables defined by the NCBI taxonomy group. The tool can also highlight the intron/exon structure of genes using information found in the feature table of GenBank flatfiles in the final translation results.

NAR Web Server Issue 2006
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tagsanimals dna sequence analysis exons initiator codon introns open reading frames protein biosynthesis ribosomes systems integration terminator codon