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Resource:ADDA - Automatic Domain Decomposition Algorithm

Name: Resource:ADDA - Automatic Domain Decomposition Algorithm
Description: This is a web interface for ADDA, an automatic algorithm for domain decomposition and clustering of all protein domain families. We use alignments derived from an all-on-all sequence comparison to define domains within protein sequences based on a global maximum likelihood model. ADDA is downloadable.

There are three ways in which you can retrieve a protein sequence and its domains from ADDA. Sequences can be located using sequence identifiers and/or accession numbers, using a identical fragment lookup, or by running BLAST against all sequences in ADDA.

ADDA is a protein sequence clustering algorithm. It takes a set of sequences and returns domain families. ADDA has two steps corresponding to the two aspects of the protein sequence clustering domain. First, ADDA splits protein sequences into domains. The idea behind ADDA is in principle the application of Occam's razor; the goal is to describe the diversity of protein sequences with a minimal set of protein domains. The algorithm behind ADDA approximates this minimal set. In practice ADDA works by looking at where BLAST alignments are located on the sequence and splits the sequences, so that as few as possible alignments are cut by domain boundaries and that as many alignments as possible stretch over complete domains. Secondly, ADDA takes all the domains and then arranges them in a minimum spanning tree, where the similarity between two domains is determined by their relative overlap given a BLAST alignment. Each link in the tree is then checked by a pairwise profile-profile comparison and links below a threshold are removed. The remaining connected components are then taken to represent protein domain families.
Other Name(s): Automatic Domain Decomposition Algorithm
Abbreviation: ADDA
Parent Organization: University of Helsinki; Helsinki; Finland
Resource Type(s): Data analysis service, Database
Resource: Resource
URL: http://ekhidna.biocenter.helsinki.fi/sqgraph/pairsdb
*Id: nif-0000-02535
PMID: PMID 12706730
Link to OWL / RDF: Download this content as OWL/RDF

Curation status: Curated

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Facts about Resource:ADDA - Automatic Domain Decomposition AlgorithmRDF feed
AbbrevADDA  +
CurationStatusuncurated  +
DefiningCitationhttp://ekhidna.biocenter.helsinki.fi/sqgraph/pairsdb  +
DefinitionThis is a web interface for ADDA, an autom This is a web interface for ADDA, an automatic algorithm for domain decomposition and clustering of all protein domain families. We use alignments derived from an all-on-all sequence comparison to define domains within protein sequences based on a global maximum likelihood model. ADDA is downloadable.

There are three ways in which you can retrieve a protein sequence and its domains from ADDA. Sequences can be located using sequence identifiers and/or accession numbers, using a identical fragment lookup, or by running BLAST against all sequences in ADDA.

ADDA is a protein sequence clustering algorithm. It takes a set of sequences and returns domain families. ADDA has two steps corresponding to the two aspects of the protein sequence clustering domain. First, ADDA splits protein sequences into domains. The idea behind ADDA is in principle the application of Occam's razor; the goal is to describe the diversity of protein sequences with a minimal set of protein domains. The algorithm behind ADDA approximates this minimal set. In practice ADDA works by looking at where BLAST alignments are located on the sequence and splits the sequences, so that as few as possible alignments are cut by domain boundaries and that as many alignments as possible stretch over complete domains. Secondly, ADDA takes all the domains and then arranges them in a minimum spanning tree, where the similarity between two domains is determined by their relative overlap given a BLAST alignment. Each link in the tree is then checked by a pairwise profile-profile comparison and links below a threshold are removed. The remaining connected components are then taken to represent protein domain families.
aken to represent protein domain families.
Has default formThis property is a special property in this wiki.Resource  +
Has roleData analysis service  +, and Database  +
Idnif-0000-02535  +
Is part ofUniversity of Helsinki; Helsinki; Finland  +
LabelResource:ADDA - Automatic Domain Decomposition Algorithm  +
ModifiedDate25 October 2012  +
PMID12706730  +
Page has default formThis property is a special property in this wiki.Resource  +
SuperCategoryResource  +
SynonymAutomatic Domain Decomposition Algorithm  +