> > Databases

Databases

This section contains databases of coding/non-coding DNA, nucleic acid and gene structure, transcriptional regulator sites, transcription factors, molecular probes, and primers.

RSS FeedCompact ViewList as XMLList as JSON

Found 54 links

Displaying 15 links

3D-FootprintDatabase Content

http://floresta.eead.csic.es/3dfootprint

DNA > Databases
Protein > Databases

3D-footprint provides estimates of binding specificity for all protein-DNA complexes available at the Protein Data Bank. The web interface allows the user to: (i) browse DNA-binding proteins by keyword; (ii) find proteins that recognize a similar DNA motif and (iii) BLAST similar DNA-binding proteins, highlighting interface residues in the resulting alignments. Comparisons with expert-curated databases RegulonDB and TRANSFAC support the quality of structure-based estimates of specificity.

This content is being maintained by brunocontreras.

NAR Database Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsanimals bacterial proteins computational biology dna-binding proteins genetic databases genetic regulation humans nucleic acid databases protein conformation protein databases protein-DNA complex pubmed regulator genes sequence alignment

3DNALandscapesDatabase Content

http://dcp.rutgers.edu

DNA > Databases

3DNALandscapes is a database for exploring the conformational features of DNA. 3DNALandscapes enables searches of conformational information across multiple structures. The database contains a wide variety of structural parameters and molecular images, computed with the 3DNA software package and known to be useful for characterizing and understanding the sequence-dependent spatial arrangements of the DNA sugar-phosphate backbone, sugar-base side groups, base pairs, base-pair steps, groove structure, etc. The data comprise all DNA-containing structures--both free and bound to proteins, drugs and other ligands--currently available in the Protein Data Bank.

NAR Database Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsanimals computational biology dna genetic databases humans ligands nucleic acid conformation nucleic acid databases protein databases

ACLAMEDatabase Content

http://aclame.ulb.ac.be/

DNA > Databases

The ACLAME database is dedicated to the collection, analysis and classification of sequenced mobile genetic elements (MGEs, in particular phages and plasmids). Classifications are available at various levels of organization. At the gene/protein level, families group similar sequences that are expected to share the same function. Families of four or more proteins are manually assigned with a functional annotation using the GeneOntology and the locally developed ontology MeGO dedicated to MGEs. At the genome level, evolutionary cohesive modules group sets of protein families shared among MGEs. At the population level, networks display the reticulate evolutionary relationships among MGEs.

NAR Database Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms bacterial genome bacteriophages computational biology genetic databases interspersed repetitive sequences nucleic acid databases nucleic acid repetitive sequences plasmids

CADgeneDatabase Content

http://www.bioguo.org/CADgene/

DNA > Databases

The CADgene, a comprehensive manually curated database for coronary artery disease genes. Candidate genes are classified into 12 functional categories based on their roles in CAD. Each gene includes detailed information from related studies (e.g. the size of case-control, population, SNP, odds ratio, P-value, etc.) and useful annotations, which include general gene information, Gene Ontology annotations, KEGG pathways, protein-protein interactions and others.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagscoronary artery disease genetic databases genetic predisposition to disease humans single nucleotide polymorphism

CCDBDatabase Content

http://crdd.osdd.net/raghava/ccdb

DNA > Databases

The Cervical Cancer gene DataBase (CCDB) is a manually curated catalog of experimentally validated genes that are thought, or are known to be involved in the different stages of cervical carcinogenesis. Each record contains details related to gene like architecture (exon-intron structure), location, function, sequences (mRNA/CDS/protein), ontology, interacting partners, homology to other eukaryotic genomes, structure and links to other public databases, thus augmenting CCDB with external data. Also, manually curated literature references have been provided to support the inclusion of the gene in the database and establish its association with cervix cancer. In addition, CCDB provides information on microRNA altered in cervical cancer as well as search facility for querying, several browse options and an online tool for sequence similarity search.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsfemale genetic databases humans neoplasm genes uterine cervical neoplasms

ChimerDBDatabase Content

http://ercsb.ewha.ac.kr/fusiongene

DNA > Databases

ChimerDB is a knowledgebase of fusion genes identified from bioinformatics analysis of transcript sequences in the GenBank and various other public resources such as the Sanger cancer genome project (CGP), OMIM, PubMed and the Mitelman's database. A new algorithm that is more sensitive, has detected 2699 fusion transcripts with high confidence. Furthermore, it can identify interchromosomal translocations as well as the intrachromosomal deletions or inversions of large DNA segments. Results from the analysis of next-generation sequencing data in the short read archives are incorporated along with a new alignment viewer.

NAR Database Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms animals chromosomes computational biology gene expression profiling genetic databases genetic translocation humans nucleic acid databases protein databases pubmed

COSMICDatabase Content

http://www.sanger.ac.uk/genetics/CGP/cosmic/

DNA > Databases
Human Genome > Databases

COSMIC curates comprehensive information on somatic mutations in human cancer. Release v48 (July 2010) describes over 136,000 coding mutations in almost 542,000 tumour samples; of the 18,490 genes documented, 4803 (26%) have one or more mutations. Full scientific literature curations are available on 83 major cancer genes and 49 fusion gene pairs. Biomart allows more automated data mining and integration with other biological databases. Annotation of genomic features has become a significant focus. COSMIC integrates many diverse types of mutation information and is making much closer links with Ensembl and other data resources.

NAR Database Issue 2010NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagscomputational biology data mining genetic databases human genome humans mutation neoplasms nucleic acid databases protein databases search engine tumor cell line

DAnCERDatabase Content

http://wodaklab.org/dancer/

DNA > Databases

The DAnCER (Disease Annotated Chromatin Epigenetic Resource) resource integrates information on genes with chromatin modification (CM) function from five model organisms, including human. Currently integrated are gene functional annotations, Pfam domain architecture, protein interaction networks and associated human diseases. Additional supporting evidence includes orthology relationships across organisms, membership in protein complexes, and information on protein 3D structure. DAnCER allows visual explorations of the integrated data and flexible query capabilities using a variety of data filters. In particular, disease information and functional annotations are mapped onto the protein interaction networks.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsanimals caenorhabditis elegans chromatin disease drosophila melanogaster epigenomics genetic databases humans mice molecular sequence annotation protein conformation protein interaction mapping saccharomyces cerevisiae

DBASS3 and DBASS5Database Content

http://www.dbass.org.uk/

DNA > Databases

DBASS3 and DBASS5 provide comprehensive repositories of new exon boundaries that were induced by pathogenic mutations in human disease genes. Aberrant 5'- and 3'-splice sites were activated either by mutations in the consensus sequences of natural exon-intron junctions (cryptic sites) or elsewhere ('de novo' sites). DBASS3 and DBASS5 data can be searched by disease phenotype, gene, mutation, location of aberrant splice sites in introns and exons and their distance from authentic counterparts, by bibliographic references and by the splice-site strength estimated with several prediction algorithms. The user can also retrieve reference sequences of both aberrant and authentic splice sites with the underlying mutation.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsdisease humans mutation nucleic acid databases rna splice sites terminology as topic

dbCRIDDatabase Content

http://dbCRID.biolead.org

DNA > Databases

A database of Chromosomal Rearrangements In Diseases (dbCRID, http://dbCRID.biolead.org) is a database of human CR events and their associated diseases. For each reported CR event, dbCRID documents the type of the event, the disease or symptoms associated, and--when possible--detailed information about the CR event including precise breakpoint positions, junction sequences, genes and gene regions disrupted and experimental techniques applied to discover/analyze the CR event.

This content is being maintained by tongbinli.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagschromosome aberrations chromosome breakpoints disease factual databases humans neoplasms

dbDNVDatabase Content

http://goods.ibms.sinica.edu.tw/DNVs/

DNA > Databases

The duplicated gene nucleotide variants database (dbDNV) (http://goods.ibms.sinica.edu.tw/DNVs/) promotes accurate variation annotation. Aside from the flat file download, users can explore the gene-related duplications and the associated DNVs by DGL and DNV searches, respectively. In addition, the dbDNV contains 304,110 DNV-coupled SNPs. From DNV-coupled SNP search, users observe which SNP records are also variants among duplicates.

This content is being maintained by wenlin.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsduplicate genes genetic variation human genome humans molecular sequence annotation nucleic acid databases single nucleotide polymorphism

dbSNP-QDatabase Content

http://cgsmd.isi.edu/dbsnpq

DNA > Databases

dbSNP-Q is a web application for working with the dbSNP relational database. dbSNP is a source of information on single nucleotide polymorphisms (SNPs) and other genetic variation for many different organisms, including humans. dbSNP-Q can be used to query human data from dbSNP for a variety tasks such as genomic mapping, SNP/gene functional properties, allele frequency data and information on the underlying experiments. It also includes documentation and download tools.

This content is being maintained by ssaccone.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagshumans nucleic acid databases single nucleotide polymorphism

DBTSSDatabase Content

http://dbtss.hgc.jp/

DNA > Databases

DataBase of Transcription Start Sites (DBTSS) is a database which contains precise positional information for transcription start sites (TSSs) of eukaryotic mRNAs. Included are 330 million new tags generated by massively sequencing the 5'-end of oligo-cap selected cDNAs in humans and mice. 31 different cell types or culture conditions are represented. Differential usage of alternative 5'-ends across cell types and conditions can be viewed in a series of new interfaces. Promoter sequence information is now displayed in a comparative genomics viewer where evolutionary turnover of the TSSs can be evaluated.

This content is being maintained by Kenta Nakai.

NAR Database Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms animals computational biology gene expression profiling genetic databases genomics humans mice nih 3t3 cells nucleic acid databases protein databases transcription initiation site

DDBJDatabase Content

http://www.ddbj.nig.ac.jp

DNA > Databases

The DNA Data Bank of Japan (DDBJ) provides a nucleotide sequence archive database and accompanying database tools for sequence submission, entry retrieval and annotation analysis. A new archive for quantitative genomics data, the DDBJ Omics aRchive (DOR). The DOR stores quantitative data both from the microarray and high-throughput new sequencing platforms. Other improvements include improved content of the DDBJ patent sequence, released a new submission tool of the DDBJ Sequence Read Archive (DRA) which archives massive raw sequencing reads, and enhanced a cloud computing-based analytical system from sequencing reads, the DDBJ Read Annotation Pipeline.

NAR Database Issue 2010NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms amino acid sequence animals bacterial genome computational biology genetic databases genomics humans japan molecular sequence annotation nucleic acid databases patents as topic protein databases

DDPCDatabase Content

http://apps.sanbi.ac.za/ddpc/

DNA > Databases

Dragon Database of Genes associated with Prostate Cancer (DDPC) as an integrated knowledgebase of genes experimentally verified as implicated in PC. DDPC is distinctive from other databases in that (i) it provides pre-compiled biomedical text-mining information on PC, which otherwise require tedious computational analyses, (ii) it integrates data on molecular interactions, pathways, gene ontologies, gene regulation at molecular level, predicted transcription factor binding sites on promoters of PC implicated genes and transcription factors that correspond to these binding sites and (iii) it contains DrugBank data on drugs associated with PC.

NAR Database Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsdata mining genetic databases humans knowledge bases male neoplasm genes prostatic neoplasms

Tags associated with subcategory 'DNA/Databases'

nucleic acid databases humans genetic databases computational biology animals protein databases genomics algorithms bacterial genome alternative splicing protein conformation protein-DNA complex sequence alignment cell nucleus regulator genes cytoplasm complementary dna pubmed 3' untranslated regions 5' untranslated regions genetic translocation chromosomes genetic regulation polyribosomes rna transcription initiation site dna-binding proteins plants ribosomal spacer dna ligands nucleic acid sequence homology fungi nucleic acid denaturation thermodynamics fungal genome nucleic acid conformation amino acid motifs mice nih 3t3 cells protein isoforms genome fungal proteins binding sites dna operon chromatin immunoprecipitation terminator codon base sequence systems integration tertiary protein structure phylogeny nucleic acids europe European Bioinformatics Institute (EBI) gene expression profiling viral genome proteins sequence analysis sequence homology National Center for Biotechnology Information (NCBI) transcriptional regulatory elements transcription factors natural language processing periodicals as topic protein binding plant genome national library of medicine (u.s.) bacteriophages interspersed repetitive sequences nucleic acid repetitive sequences prokaryotic cells united states molecular sequence data protein biosynthesis ribosomal frameshifting plasmids biotechnology metagenomics molecular sequence annotation national institutes of health (u.s.) high-throughput nucleotide sequencing japan factual databases patents as topic dna sequence analysis archaeal genome phenotype inborn genetic diseases india mutation european continental ancestry group insect genes genetic terminator regions drosophila drosophila proteins tumor cell line nucleic acid regulatory sequences genetic predisposition to disease female neoplasm genes coronary artery disease