Domains and Motifs

This section includes links to tools which can give information about protein domains and/or predict motifs, domains, and patterns in peptide sequences.

Found 153 links

Displaying 15 links

3MatrixTool Content

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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.

This content is being maintained by brutlag.

AIDATool Content

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AIDA: Ab Initio Domain Assembly Server attempts to find the best domain arrangements while maintaining chain connectivity. The server also supports structure assembly from sequence only and restraint-guided simulation producing a final assembly satisfying user-specified inter-domain distance restraints.

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ASEBTool Content

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Acetylation Set Enrichment Based (ASEB) computational tool predicts which K-acetyl-transferase families are responsible for the acetylation of a given protein or lysine site. Other information such as protein-protein interaction information is used to enhance prediction accuracy.

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AUGUSTUSTool Content

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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.

Berkeley Phylogenomics GroupTool Content

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The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.

This content is being maintained by kimmen.

Blocks WWW ServerTool Content

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The Blocks WWW server provides tools to search DNA and protein queries against the Blocks database of multiple alignments, which represent conserved protein regions.

CD-SearchDatabase Content

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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.

This content is being maintained by Aron Marchler-Bauer.

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