> Tag > Links tagged with 'rna splicing'

Links tagged with 'rna splicing'

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Found 8 links

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AGenDATool Content

http://bibiserv.techfak.uni-bielefeld.de/agenda/ [open in a new window]

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DNA > Gene Prediction
Sequence Comparison > Analysis of Aligned Sequences

AGenDA is a web tool that compares the genomic sequences from evolutionarily related organisms in order to make gene predictions. It takes pairs of genomic sequences as input, aligns the sequences, and makes predictions based on splice signals, start and stop codons, and areas of conserved sequence.

links directory index: 11
TitlePublication YearGoogle Scholar Citation Count
AGenDA: gene prediction by cross-species sequence comparison200411
NAR Web Server Issue 2004
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tagsanimals base sequence conserved sequence dna footprinting dna sequence analysis genes genomics humans mice nucleic acid sequence homology phylogeny rna splicing sequence alignment

AHD2.0Database Content

http://ahd.cbi.pku.edu.cn/ [open in a new window]

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Model Organisms > Databases

Arabidopsis Hormone Database (AHD) is a collection of hormone related genes of the model organism Arabidopsis thaliana (AHRGs). AHD2.0 has new features: (i) updating our collection of AHRGs based on most recent publications as well as constructing elaborate schematic diagrams of each hormone biosynthesis and signaling pathways; (ii) adding orthologs of sequenced plants listed in OrthoMCL-DB to each AHRG in the updated database; (iii) providing predicted miRNA splicing site(s) for each AHRG; (iv) integrating genes that genetically interact with each AHRG according to literatures mining; (v) providing links to a powerful online analysis platform WebLab for the convenience of in-time bioinformatics analysis and (vi) providing links to widely used protein databases and integrating more expression profiling information that would facilitate users for a more systematic and integrative analysis related to phytohormone research.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
AHD2.0: an update version of Arabidopsis Hormone Database for plant systematic studies20112
NAR Database Issue 2011
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tagsarabidopsis genetic databases micrornas plant genes plant growth regulators rna splicing

ERANGETool Content

http://woldlab.caltech.edu/rnaseq/ [open in a new window]

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Expression > Gene Regulation

A package of python scripts designed to analyze ultra-high-througphut sequencing data from the Illumina/Solexa platform for RNA-seq and ChIP-seq in metazoan genomes. The RNA-seq portion of ERANGE is described in our Nature Methods paper "Mapping and quantifying mammalian transcriptomes by RNA-Seq" (Mortazavi, 2008). ERANGE is built on top of Cistematic.

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tags3' untranslated regions algorithms alternative splicing animals brain chromosome mapping exons gene expression profiling genetic promoter regions inbred c57bl mice liver messenger rna mice nucleic acid databases oligonucleotide array sequence analysis rna rna sequence analysis rna splicing sensitivity and specificity skeletal muscle software

ESEfinderTool Content

http://rulai.cshl.edu/tools/ESE/ [open in a new window]

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Expression > Splicing

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

links directory index: 794
TitlePublication YearGoogle Scholar Citation Count
ESEfinder: A web resource to identify exonic splicing enhancers2003794
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

GENSCANTool Content

http://genes.mit.edu/GENSCAN.html [open in a new window]

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DNA > Gene Prediction

Identification of complete gene structures in genomic DNA.

links directory index: 3198
TitlePublication YearGoogle Scholar Citation Count
Finding the genes in genomic DNA1998404
Prediction of complete gene structures in human genomic DNA19972794
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external linksLink on Wikipedia
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

Netgene2Tool Content

http://www.cbs.dtu.dk/services/NetGene2/ [open in a new window]

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Expression > Splicing

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

links directory index: 447
TitlePublication YearGoogle Scholar Citation Count
Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information1996447
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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

Rescue-ESETool Content

http://genes.mit.edu/burgelab/rescue-ese/ [open in a new window]

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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.

links directory index: 785
TitlePublication YearGoogle Scholar Citation Count
RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons2004150
Predictive identification of exonic splicing enhancers in human genes2002635
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

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

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