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http://cryptodb.org/cryptodb/

An integrated genomic and functional genomic database for the parasite Cryptosporidium. CryptoDB integrates whole genome sequence and annotation along with experimental data and environmental isolate sequences provided by community researchers. The database includes supplemental bioinformatics analyses and a web interface for data-mining. Organisms included in CryptoDB are Cryptosporidium parvum, Cryptosporidium hominis, Cryptosporidium muris and environmental isolate sequences from numerous species. CryptoDB is allied with the databases PlasmoDB and ToxoDB via ApiDB, an NIH/NIAID-funded Bioinformatics Resource Center. Tools include: * BLAST: Identify Sequence Similarities * Sequence Retrieval: Retrieve Specific Sequences using IDs and coordinates * PubMed and Entrez: View the Latest Cryptosporidium Pubmed and Entrez Results * Genome Browser: View Sequences and Features in the genome browser * CryptoCyc: Explore Automatically Defined Metabolic Pathways * Searches via Web Services: Web service access to our data

Proper citation: ApiDB CryptoDB (RRID:SCR_013455) Copy   

•   Source: SciCrunch Registry

http://snpeff.sourceforge.net/SnpSift.html

Software toolkit for filtering and manipulating annotated files. After annotation, the software's filter function can find relevant genomic variants in large data files.

Proper citation: SnpSift (RRID:SCR_015624) Copy   

•   Source: SciCrunch Registry

https://opentrials.net/

Database that contains data such as registry entries, portions of regulatory documents describing individual trials, structured data on methods and results, and researchers and papers from and/or related to clinical trials. The initiative aims to locate, match, and share all publicly accessible data and documents, on all trials conducted, on all medicines and other treatments, globally.

Proper citation: Open Trials (RRID:SCR_015570) Copy   

•   Source: SciCrunch Registry

http://gnomad.broadinstitute.org/

Database that aggregates exome and genome sequencing data from large-scale sequencing projects. The gnomAD data set contains individuals sequenced using multiple exome capture methods and sequencing chemistries. Raw data from the projects have been reprocessed through the same pipeline, and jointly variant-called to increase consistency across projects.

Proper citation: Genome Aggregation Database (RRID:SCR_014964) Copy   

•   Source: SciCrunch Registry

https://github.com/stamatak/ExaML

Source code for large-scale phylogenetic analyses on whole-transcriptome and whole-genome alignments using supercomputers.

Proper citation: Examl (RRID:SCR_016087) Copy   

•   Source: SciCrunch Registry

http://www.lncrnadb.org/

Searchable database of comprehensive annotations of eukaryotic long non-coding RNAs. Entries are manually curated from referenced literature.

Proper citation: lncRNAdb (RRID:SCR_015491) Copy   

•   Source: SciCrunch Registry

https://web.expasy.org/abcd/

Repository of sequenced antibodies, integrating curated information about antibody and its antigen with cross links to standardized databases of chemical and protein entities. Manually curated repository of sequenced antibodies, developed by Geneva Antibody Facility at University of Geneva, in collaboration with CALIPHO and Swiss Prot groups at SIB Swiss Institute of Bioinformatics. Database provides list of sequenced antibodies with their known targets. Each antibody is assigned unique ID number that can be used in academic publications to increase reproducibility of experiments.

Proper citation: ExPASy ABCD database (RRID:SCR_017401) Copy   

•   Source: SciCrunch Registry

http://smithlabresearch.org/software/methbase/

Central reference methylome database created from public BS-seq datasets. Provides methylation level at individual sites, regions of allele specific methylation, hypo- or hyper-methylated regions, partially methylated regions, and detailed meta data and summary statistics.

Proper citation: MethBase (RRID:SCR_017487) Copy   

•   Source: SciCrunch Registry

https://signalingpathways.org

Web multi omics knowledgebase based upon public, manually curated transcriptomic and cistromic datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Integrated omics knowledgebase for mammalian cellular signaling pathways. Web browser interface was designed to accommodate numerous routine data mining strategies. Datasets are biocurated versions of publically archived datasets and are formatted according to recommendations of the FORCE11 Joint Declaration on Data Citation Principles73, and are made available under Creative Commons CC 3.0 BY license. Original datasets are available.

Proper citation: Signaling Pathways Project (RRID:SCR_018412) Copy   

•   Source: SciCrunch Registry

https://www.zbh.uni-hamburg.de/en/forschung/gi/software/ltrsift.html

Software graphical desktop tool for semi-automatic postprocessing of de novopredicted LTR retrotransposon annotations, such as the ones generated by LTRharvestand LTRdigest. Interface displays LTR retrotransposon candidates, their putative families and their internal structure in a hierarchical fashion allowing the user to "sift" through results of de novo prediction software. It also offers customizable filtering and classification functionality.

Proper citation: LTRsift (RRID:SCR_024098) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/phenofam/

A web-based application that performs gene set enrichment analysis (GSEA) by employing structural and functional information on families of protein domains as annotation terms.

Proper citation: PhenoFam (RRID:SCR_000640) Copy   

•   Source: SciCrunch Registry

http://faculty.washington.edu/browning/floss/floss.htm

Software application that performs ordered subset analysis using MERLIN's ouput .lod file created with the --perFamily option. Ordered subset analysis uses covariate information to identify a more homogenous subset of families for linkage analysis. The homogeneous subset of families does not need to be specified a priori, and the covariates can include environmental exposures, quantitative traits, or linkage scores at another locus in the genome. The evidence for linkage is evaluated with a permutation test. (entry from Genetic Analysis Software)

Proper citation: FLOSS (RRID:SCR_000836) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/ReadqPCR.html

A software package that provides functions to read raw RT-qPCR data of different platforms.

Proper citation: ReadqPCR (RRID:SCR_000030) Copy   

•   Source: SciCrunch Registry

http://mzmatch.sourceforge.net/

A software to provide small tools for common processing tasks for LC/MS data. It is an extension to the metabolomics analysis pipeline mzMatch.R. The software is modular, open source, platform independent and written in Java.

Proper citation: mzMatch (RRID:SCR_000543) Copy   

•   Source: SciCrunch Registry

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

A database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. In addition to provide information on the full genomes and genetic entities, it aims at building a comprehensive classification of the functional modules of MGE's at the protein, gene, and higher levels. Prophinder, a tool dedicated to the detection of prophages in sequenced bacterial genomes, is available on ACLAME.

Proper citation: A Classification of Mobile genetic Elements (RRID:SCR_001694) Copy   

•   Source: SciCrunch Registry

http://www.cisred.org/

Database for conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations. Sequence inputs include low-coverage genome sequence data and ENCODE data. The database offers information on atomic motifs, motif groups and patterns. In promoter-based cisRED databases, sequence search regions for motif discovery extend from 1.5 Kb upstream to 200b downstream of a transcription start site, net of most types of repeats and of coding exons. Many transcription factor binding sites are located in such regions. For each target gene's search region, a base set of probabilistic ab initio discovery tools is used, in parallel, to find over-represented atomic motifs. Discovery methods use comparative genomics with over 40 vertebrate input genomes. In ChIP-seq-based cisRED databases, sequence search regions for motif discovery correspond to significant peaks that represent genome-wide sites of protein-DNA binding. Because such peaks occur in a wide range of genic and intergenic locations, ChIP-seq and promoter-based databases are complementary. Currently, motif discovery for ChIP-seq data uses scan-based approaches that make more explicit use of sets of sequences known to be functional transcription factor binding sites, and that consider a wide range of levels of conservation. For the human STAT1 ChIP-seq database search regions in the target species (human) was selected +/- 300 bp around the ChIP-seq peak maximum. Repeats and coding regions were masked. Multiple sequence alignment were used to assemble orthologous input sequences from other species.

Proper citation: cisRED: cis-regulatory element (RRID:SCR_002098) Copy   

•   Source: SciCrunch Registry

http://cbrc.kaust.edu.sa/tcof/

Database that facilitates the exploration of proteins involved in the regulation of transcription in humans by binding to regulatory DNA regions (transcription factors) and proteins involved in the regulation of transcription in humans by interacting with transcription factors and not binding to regulatory DNA regions (transcription co-factors).

Proper citation: TcoF (RRID:SCR_002158) Copy   

•   Source: SciCrunch Registry

http://bisc.soe.ucsc.edu/

A protein-protein interaction (PPI) database intending to bridge between the two communities most active in their characterization: structural biology and functional genomics researchers. It offers users access to binary subcomplexes, (i.e. physical direct interactions between proteins) that are either structurally characterized or modellable entries in the main functional genomics PPI databases BioGRID, IntAct and HPRD. Selected web services are available to further investigate the validity of postulated PPI by inspection of their hypothetical modelled interfaces., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BISC (RRID:SCR_002064) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/astd/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Alternative Splicing and Transcript Diversity (ASTD) database project is creating a database of alternative splice events and transcripts of genes from human, mouse and rat. Full length transcripts are generated with the aim of understanding the mechanism of alternative splicing on a genome-wide scale. The current release of the human genome consists of: 16715 genes, 14101 have more than one splice isoform, with an average of 5.6 splice patterns per gene. 10831 transcripts are annotated as full length with a transcription start site and a poly(A). The current release of the mouse genome consists of: 16491 genes, 13028 have more than one splice isoform, with an average of 4 splice patterns per gene. 6011 transcripts are annotated as full length with a transcription start site and a poly(A). The current release of the rat genome consists of: 10424 genes, 6344 have more than one splice isoform, with an average of 2.6 splice patterns per gene. 1250 transcripts are annotated as full length with a transcription start site and a poly(A). Sponsors: The ASTD project at EBI is supported by a grant from the EC: Eurasnet Network of Excellence (LSHG-CT-2005-518238). It was also supported by the ASD grant from the EC (QLRT-CT-2001-02062) until November 2005 and the ATD grant from the EC (LSHG-CT-2003-503329) until May 2007.

Proper citation: The Alternatve Splicing Database (RRID:SCR_001883) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/chebi/beta/

Collection of chemical compounds and other small molecular entities that incorporates an ontological classification of chemical compounds of biological relevance, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.

Proper citation: CHEBI (RRID:SCR_002088) Copy   

•   Source: SciCrunch Registry