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[21 MAR 2013] A new version of the Conserved Domain Database (CDD) has been released. Version 3.10 contains 1104 new or updated NCBI-curated domain models. Also, position-specific score matrices have been re-computed for a large fraction of the models in CDD, which has slightly affected the resulting sequence annotations. PSSMs are now provided in an extended format. They contain 28 rows instead of 26, and also come with intermediate data in addition to the final scoring matrix. The latter will make it possible to directly generate search databases for the current version of RPS-BLAST, DELTA-BLAST, as well as an upcoming new version of RPS-BLAST that supports composition-corrected scoring. Click on the database statistics at the right to retrieve the subset of records from any source database.
[06 AUG 2012] A specific hit is a high confidence association between a protein query sequence and a conserved domain, resulting in a high confidence level for the inferred function of the protein query sequence. The algorithm for identifying specific hits has been revised to include domain models from external sources. Previously, specific hits were limited to NCBI-curated domains. Now, if domain models from both the NCBI-curated data set and external sources meet a domain-specific threshold, the NCBI-curated domain will still be listed preferentially as the specific hit because it has been annotated with fine-grained evolutionary relationships, conserved sequence blocks, specific functions, and conserved features/sites based on careful review of sequence data, 3D structures, and literature. However, if no NCBI-curated domain meets the criteria for a specific hit, then the top-ranked domain model from an external source will be shown in the CD-Search results concise display if it meets all the criteria for a specific hit. As a result of this change, more sequences in the Entrez Protein database are now annotated with specific functional information.Database Statistics
[17 SEP 2012] The CDD v3.08 release includes 239 new or updated NCBI-curated domains.
[06 AUG 2012] The CDD v3.07 release includes 495 new or updated NCBI-curated domains.
[29 MAY 2012] The CDD v3.06 release includes 310 new or updated NCBI-curated domains.
[28 MAR 2012] Conserved Domain searches are now being launched for all nucleotide queries shorter than 10,000 base pairs submitted to blastx, the BLAST program that translates a nucleotide query sequence in six reading frames and compares each translation against the protein data set. The blastx search results page includes a concise display of the conserved domains found on the translated reading frames, and that graphic links to the corresponding interactive view in the CD-Search tool.
[08 MAR 2012] The CDD v3.04 release includes 166 new or updated NCBI-curated domain models..
[09 NOV 2011] The CDD v3.01 release includes 298 new or updated NCBI-curated domains.
[04 NOV 2011] The CD-Search tool now accepts nucleotide sequences as queries. It translates them in all six reading frames and searches each protein product against the RPS-BLAST databases. CD-Search will combine the results for all the proteins into a single page, but will only display the translated reading frames that picked up a match in CDD. The help document provides additional details.
[28 Oct 2011] The CDD v3.00 release contains the same conserved domain models as the previous release (CDD v2.32). However, the composition of some superfamily clusters have changed, and the single domain/ multidomain status assigned to some conserved domain models has also changed. These changes are due to a slightly revised E-value calculation implemented in the BLAST program suite (including RPS-BLAST), which now uses a new variant of the Finite Size Correction that produces more accurate E-values for short query and/or subject sequences.
[05 OCT 2011] A new release of the Conserved Domain Architecture Retrieval Tool (CDART) is available and offers new functions and features for finding proteins that have domain architectures similar to a query protein ( illustrated example):
[02 SEP 2011] The CDD v2.32 release includes 14 new or updated NCBI-curated domains, suppresses pfam10695, and fixes errors in superfamily clustering.
[25 JULY 2011] The Conserved Domain Database now has a revised home page, search interface, and search results display, to have functions similar to those available in PubMed. Changes include: (a) a streamlined home page with links to related resources; (b) an "Advanced Search" page, which provides the ability to build a query one term at a time, browse the index of any search field, and combine earlier searches; and (c) new search results displays that provide links in the right margin to search filters, related data, and tools.
[16 JUN 2011] The CDD v2.30 release includes 201 new or updated NCBI-curated domains.
[02 MAR 2011] The CDD v2.27 release includes 357 new or updated NCBI-curated domains.
[07 OCT 2010] The CDD v2.25 release includes 88 new or updated NCBI-curated domains.
[30 SEP 2010] A Batch CD-Search tool is now available for the computation and download of conserved domain annotation on large sets of protein queries. Input up to 100,000 protein query sequences as a list of sequence identifiers and/or raw sequence data, then download output in a variety of formats (including tab-delimited text files) or view the search results graphically. See the help document for additional details, including information on using Batch CD-Search for scripted data downloads.
[09 SEP 2010] The CDD v2.24 release includes 196 new or updated NCBI-curated domains.
[29 JUL 2010] The CDD v2.23 release includes 174 new or updated NCBI-curated domains.
[26 MAY 2010] The CDD v2.22 release includes 443 new or updated NCBI-curated domains.
[13 APR 2010] The CDD v2.21 release includes 489 new or updated NCBI-curated domains as well as the most recent data from PRK, which now includes domain models for plant-specific (non-chloropast) proteins, indicated by PLN accession number prefixes.
[10 DEC 2009] The CDD v2.18 release includes 489 new or updated NCBI-curated domains.
[04 JUN 2009] The CDD v2.17 release includes 484 new or updated NCBI-curated domains, as well as records from a new data source, TIGRFAM, and protozoan domains from the Protein Clusters (PRK) database.
[08 MAY 2008] The CD-Search tool now shows four types of hits in search results, including specific hits. A specific hit is a high confidence association between a protein query sequence and a conserved domain, resulting in a high confidence level for the inferred function of the protein query sequence. more...
[08 MAY 2008] The Conserved Domain Database (CDD) is now organized into superfamilies. A superfamily cluster is a set of conserved domain models that generate overlapping annotation on the same protein sequences. These models are assumed to represent evolutionarily related domains and may be redundant with each other. more...| Revised 21 March 2013 | | Help Desk | Disclaimer | Privacy statement | Accessibility |
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