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Links tagged with 'dna footprinting'

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AGenDATool Content

http://bibiserv.techfak.uni-bielefeld.de/agenda/

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.

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

CONREALTool Content

http://conreal.niob.knaw.nl/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

CONREAL (Conserved Regulatory Elements Anchored Alignment) allows identification of transcription factor binding sites (TFBS) that are conserved between two orthologous promoter sequences.

NAR Web Server Issue 2005
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tagsalgorithms animals base sequence binding sites conserved sequence dna footprinting dna sequence analysis dna-binding proteins gene expression regulation genetic promoter regions hepatocyte nuclear factor 3-beta humans mice nuclear proteins nucleic acid regulatory sequences nucleic acid sequence homology phylogeny rats sequence alignment takifugu transcription factors zebrafish

ConsiteTool Content

http://www.phylofoot.org/consite/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Detect transcription factor binding sites in genomic sequences using phylogenetic footprinting and experimentally-confirmed binding profiles.

NAR Web Server Issue 2004
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tagsalgorithms animals binding sites computational biology conserved sequence dna dna footprinting dna sequence analysis genetic models human genome humans nucleic acid regulatory sequences phylogeny predictive value of tests regulator genes sensitivity and specificity sequence alignment transcription factors

Drosophila DNase I footprint databaseDatabase Content

http://www.flyreg.org/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Model Organisms > Fly

Database of transcription factor binding sites created from systematic literature curation and genome annotation of DNase I footprints for Drosophila.

This content is being maintained by caseybergman.

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tagsbinding sites dna footprinting drosophila genome annotation transcription factors
setsUniversity of Manchester

FooterTool Content

http://biodev.hgen.pitt.edu/Footer/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Footer is a tool for identifying highly-probable binding sites of known transcription factors using phylogenetic footprinting principles to analyse two homologous DNA sequences.

NAR Web Server Issue 2005
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tagsalgorithms animals binding sites dna footprinting dna sequence analysis gene expression regulation genetic promoter regions mammals phylogeny transcription factors

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