3Matrix is a tool for visualizing protein sequence motifs and their properties in 3 dimensions. This tool needs to be downloaded and run locally on your own machine.
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.
ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.
AREsite is an online resource for the detailed investigation of AU-rich elements (ARE) in vertebrate mRNA 3'-untranslated regions (UTRs). AREsite allows one to quantify the structuredness of ARE motif sites in terms of opening energies and accessibility probabilities. A detailed phylogenetic analysis of ARE motifs and incorporate information about experimentally validated targets of the ARE-binding proteins TTP, HuR and Auf1 is also provided.
Server which scans upstream of genes in the same gene expression cluster for regulatory sequence motifs using a Gibbs sampling strategy. The Markov background model is used for non-motif bases, improving specificity of predicted motif locations.
CD-Search allows the user to search the Conserved Domain Database (CDD) for conserved structural and functional domains in a sequence of interest; links to 3-D structures where applicable.
NCBI's Conserved Domain Database (CDD) is a resource for the annotation of protein sequences with the location of conserved domain footprints, and functional sites inferred from these footprints. CDD includes manually curated domain models that make use of protein 3D structure to refine domain models and provide insights into sequence/structure/function relationships.
CisMols (Cis-regulatory Modules) is a tool that identifies compositionally predicted cis-clusters that occur in groups of co-regulated genes within each of their ortholog-pair evolutionarily conserved cis-regulatory regions.
COLORADO-3D allows you to color your protein structures to indicate the presence of potential errors in protein structure (detected by ANOLEA, PROSAII, PROVE or VERIFY3D), buried residues, and sequence conservation. The server returns a PDB-formatted file which can be displayed in RASMOL.
Server which attempts to identify any motifs related to genes predicted to share regulatory elements. It alters Gibbs sampling through biasing searches towards conserved sequences across multiple species.
CONREAL (Conserved Regulatory Elements Anchored Alignment) allows identification of transcription factor binding sites (TFBS) that are conserved between two orthologous promoter sequences.
134 Resources
