EditFrom NeuroLex
(Redirected from Category:Resource: ADDA - Automatic Domain Decomposition Algorithm)
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 |
| Parent Organization: | University of Helsinki; Helsinki; Finland |
| Resource Type(s): | Data analysis service, Database |
| Abbreviation: | ADDA |
| Resource: | Resource |
| URL: | http://ekhidna.biocenter.helsinki.fi/sqgraph/pairsdb |
| PMID: | PMID 12706730 |
| Id: | nif-0000-02535 |
| Link to OWL / RDF: | Download this content as OWL/RDF |
Curation status: Curated
For Resource Owners:
A sitemap will keep your NIF Registry description up-to-date and inform search engines about your resource.
Please login to create the sitemap. (top right)
Learn more about what NIF can do for your resource.
Proudly proclaim your inclusion in NIF by displaying the "Registered with NIF" button on your site.
Notes
This page uses this default form:Resource
Facts about Resource:ADDA - Automatic Domain Decomposition AlgorithmRDF feed
| Abbrev | ADDA + |
| CurationStatus | uncurated + |
| DefiningCitation | http://ekhidna.biocenter.helsinki.fi/sqgraph/pairsdb + |
| Definition | This 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 role | Data analysis service +, and Database + |
| Id | nif-0000-02535 + |
| Is part of | University of Helsinki; Helsinki; Finland + |
| Label | Resource:ADDA - Automatic Domain Decomposition Algorithm + |
| ModifiedDate | 25 October 2012 + |
| PMID | 12706730 + |
| Page has default formThis property is a special property in this wiki. | Resource + |
| SuperCategory | Resource + |
| Synonym | Automatic Domain Decomposition Algorithm + |