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http://unicarb-db.biomedicine.gu.se
An experimental glycomic MS database initially created to meet the in-house need to store structural and MS-glycomic data. Users can search by taxonomy and tissue, mass and composition, and MS/MS.
Proper citation: UniCarb-DB (RRID:SCR_014407) Copy
A genome and functional genomic database for the protozoan parasite Toxoplasma gondii. It incorporates the sequence and annotation of the T. gondii ME49 strain, as well as genome sequences for the GT1, VEG and RH (Chr Ia, Chr Ib) strains. Sequence information is integrated with various other genomic-scale data, including community annotation, ESTs, gene expression and proteomics data. Organisms * Toxoplasma gondii (ME49, RH, GT1, Veg strains) * Neospora caninum * environmental isolate sequences from numerous species Tools * BLAST: Identify Sequence Similarities * Sequence Retrieval: Retrieve Specific Sequences using IDs and coordinates * PubMed and Entrez: View the Latest Toxoplasma, Neospora Pubmed and Entrez Results * Genome Browser: View Sequences and Features in the genome browser * Ancillary Genome Browse: Access Additional info like Probeset data and Toxoplasma Array info
Proper citation: ApiDB ToxoDB (RRID:SCR_013453) Copy
The HUGE protein database has been created to publicize the Human cDNA project at the Kazusa DNA Research Institute. This project will sequence and analyze long (>4 kb) human cDNAs and establish methods by using the sequence data how to predict the primary structure of proteins of various biological activities. Currently, it focuses on the analysis of cDNA clones encoding particularly large proteins (>50 kDa). The HUGE protein database contains various types of information derived from the predicted primary structure data of newly identified human proteins. The HUGE protein database are expected to cover various sets of large human proteins of hitherto unidentified functions. They are likely to be involved in cellular structure/motility (such as cytoskeleton, membrane skeleton, and motor proteins), gene expression and nucleic acid metabolism, cell signaling/communication (such as cellular adhesion, signal transduction, channels, and receptors), and so on.
Proper citation: HUGE - Human Unidentified Gene-Encoded large proteins (RRID:SCR_013482) Copy
http://db.systemsbiology.net/kaviar/
A database containing a compilation of SNVs, indels, and complex variants observed in humans, designed to facilitate testing for the novelty and frequency of observed variants.
Proper citation: KAVIAR (RRID:SCR_013737) Copy
A database of protein disorder and mobility annotations. The database features three levels of annotation: manually curated data (which are extracted from the DisProt database), indirect data, and predicted data. Additional annotations are included from external sources, including UniProt, Pfam, PDB, and STRING.
Proper citation: MobiDB (RRID:SCR_014542) Copy
https://rtips.cancer.gov/rtips/index.do
Database of cancer control interventions and program materials. It is designed to provide program planners and public health practitioners easy and immediate access to research-tested materials.
Proper citation: Research-tested Intervention Programs (RTIPs) (RRID:SCR_016042) Copy
http://floresta.eead.csic.es/3dfootprint
Database of DNA-binding protein structures that is updated with Protein Data Bank complexes. It provides structure-based binding specificities and sequence logos, classification and clusters of protein-DNA interfaces, and downloads/stats.
Proper citation: 3D-footprint (RRID:SCR_015713) Copy
Database for the identification of the human proteome and its use across the scientific community. Users can browse proteins and chromosomes and contribute to the data repository.
Proper citation: ProteomicsDB (RRID:SCR_015562) Copy
http://amp.pharm.mssm.edu/datasets2tools/
Database for the discovery and evaluation of biomedical digital objects. It includes a wide variety of enrichment analyses, gene interaction networks, interactive data visualizations, datasets, and computational tools.
Proper citation: Datasets2Tools (RRID:SCR_016174) Copy
Collection of transcription factor microRNA regulations. TransmiR v2.0 manually curated TF-miRNA regulations from publications during 2013-2017 and included ChIP-seq-derived TF-miRNA regulation data.
Proper citation: TransmiR (RRID:SCR_017499) Copy
Collection of chemical compounds and associated information that were automatically extracted by text mining content of PubMed and PubChem databases. Unifies chemical lists from metabolomics, systems biology, environmental epidemiology, occupational expossure, toxiology and nutrition fields.
Proper citation: Blood Exposome Database (RRID:SCR_017610) Copy
Software package for nucleic acid folding and hybridization prediction. It has capabilities to predict folding for single-stranded RNA or DNA through a combination of free energy minimization, partition function calculations and stochastic sampling. The program runs on Unix and Linux platforms as well as Mac OS X and Windows.
Proper citation: UNAFold (RRID:SCR_001360) Copy
http://bioconductor.org/packages/release/bioc/html/DESeq.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Software for differential gene expression analysis based on the negative binomial distribution. It estimates variance-mean dependence in count data from high-throughput sequencing assays and tests for differential expression.
Proper citation: DESeq (RRID:SCR_000154) Copy
https://sourceforge.net/projects/popbam/
A tool to perform evolutionary or population-based analyses of next-generation sequencing data. POPBAM takes a BAM file as its input and can compute many widely used evolutionary genetics measures in sliding windows across a genome.
Proper citation: POPBAM (RRID:SCR_000464) Copy
http://code.google.com/p/gasv/
Software tool for identifying structural variants (SVs) from paired-end sequencing data.GASV distribution includes three components that are typically run in succession: the BAM file of unique paired-read mappings is processed; structural variants are identified by clustering discordant fragments; and a probabilistic algorithm improves the specificity of GASV predictions.
Proper citation: GASV (RRID:SCR_000061) Copy
http://noble.gs.washington.edu/proj/percolator/
Percolator post-processes the results of a shotgun proteomics database search program, re-ranking peptide-spectrum matches so that the top of the list is enriched for correct matches. Shotgun proteomics uses liquid chromatography-tandem mass spectrometry to identify proteins in complex biological samples. We describe an algorithm, called Percolator, for improving the rate of peptide identifications from a collection of tandem mass spectra. Percolator uses semi-supervised machine learning to discriminate between correct and decoy spectrum identifications, correctly assigning peptides to 17% more spectra from a tryptic dataset and up to 77% more spectra from non-tryptic digests, relative to a fully supervised approach. The yeast-01 data is available in tab delimetered format. The SEQUEST parameter file and target database for the yeast and worm data are also available.
Proper citation: Percolator: Semi-supervised learning for peptide identification from shotgun proteomics datasets (RRID:SCR_005040) Copy
http://corneliu.henegar.info/FunCluster.htm
FunCluster is a genomic data analysis algorithm which performs functional analysis of gene expression data obtained from cDNA microarray experiments. Besides automated functional annotation of gene expression data, FunCluster functional analysis aims to detect co-regulated biological processes through a specially designed clustering procedure involving biological annotations and gene expression data. FunCluster''''s functional analysis relies on Gene Ontology and KEGG annotations and is currently available for three organisms: Homo Sapiens, Mus Musculus and Saccharomyces Cerevisiae. FunCluster is provided as a standalone R package, which can be run on any operating system for which an R environment implementation is available (Windows, Mac OS, various flavors of Linux and Unix). Download it from the FunCluster website, or from the worldwide mirrors of CRAN. FunCluster is provided freely under the GNU General Public License 2.0. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Proper citation: FunCluster (RRID:SCR_005774) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data, but also supporting analysis of other types of data. QIMME analyzes and transforms raw sequencing data generated on Illumina or other platforms to publication quality graphics and statistics.
Proper citation: QIIME (RRID:SCR_008249) Copy
https://github.com/lpantano/seqbuster
Software tool for processing and analysis of small RNAs datasets.Reveals ubiquitous miRNA modifications in human embryonic cells.
Proper citation: SeqBuster (RRID:SCR_009616) Copy
http://www.sph.umich.edu/csg/abecasis/MACH/download/
QTL analysis based on imputed dosages/posterior_probabilities.
Proper citation: MACH (RRID:SCR_009621) Copy
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