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http://cgi-www.daimi.au.dk/cgi-chili/datfap/frontdoor.py
A database of transcription factors from 13 plant species, and PCR primers for around 90% of them.
Proper citation: DATFAP (RRID:SCR_005413) Copy
http://bioinfozen.uncc.edu/tfindit/
A database and web service for structural bioinformatics studies of transcription factor (TF)-DNA interactions. Various datasets can be generated based on one or more search options specified by users.
Proper citation: TFinDIT (RRID:SCR_005411) Copy
http://the_brain.bwh.harvard.edu/uniprobe/
Database that hosts experimental data from universal protein binding microarray (PBM) experiments (Berger et al., 2006) and their accompanying statistical analyses from prokaryotic and eukaryotic organisms, malarial parasites, yeast, worms, mouse, and human. It provides a centralized resource for accessing comprehensive data on the preferences of proteins for all possible sequence variants ("words") of length k ("k-mers"), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. The database's web tools include a text-based search, a function for assessing motif similarity between user-entered data and database PWMs, and a function for locating putative binding sites along user-entered nucleotide sequences.
Proper citation: UniPROBE (RRID:SCR_005803) Copy
http://gopubmed.org/web/gopubmed/
A web server which allows users to explore PubMed search results with the Gene Ontology, a hierarchically structured vocabulary for molecular biology. GoPubMed submits a user''''s keywords to PubMed, retrieves the abstracts, detects Gene Ontology terms in the abstracts, displays the subset of Gene Ontology relevant to the original query, and allows the user to browse through the ontology displaying associated papers and their GO annotation. Platform: Online tool
Proper citation: GoPubMed (RRID:SCR_005823) Copy
A next-generation web-based application that aims to provide an integrated solution for both visualization and analysis of deep-sequencing data, along with simple access to public datasets.
Proper citation: Systems Transcriptional Activity Reconstruction (RRID:SCR_005622) Copy
http://mint.bio.uniroma2.it/virusmint/
A virus protein interactions database that collects and annotates all the interactions between human and viral proteins and integrates this information in the human protein interaction network. It uses the PSI-MI standard and is fully integrated with the MINT database. You can search for any viral or human protein by entering either common names or database identifiers or display a complete viral interactome.
Proper citation: VirusMINT (RRID:SCR_005987) Copy
http://www.gene-regulation.com/pub/databases.html#transfac
Manually curated database of eukaryotic transcription factors, their genomic binding sites and DNA binding profiles. Used to predict potential transcription factor binding sites.
Proper citation: TRANSFAC (RRID:SCR_005620) Copy
http://www.informatics.jax.org
International database for laboratory mouse. Data offered by The Jackson Laboratory includes information on integrated genetic, genomic, and biological data. MGI creates and maintains integrated representation of mouse genetic, genomic, expression, and phenotype data and develops reference data set and consensus data views, synthesizes comparative genomic data between mouse and other mammals, maintains set of links and collaborations with other bioinformatics resources, develops and supports analysis and data submission tools, and provides technical support for database users. Projects contributing to this resource are: Mouse Genome Database (MGD) Project, Gene Expression Database (GXD) Project, Mouse Tumor Biology (MTB) Database Project, Gene Ontology (GO) Project at MGI, and MouseCyc Project at MGI.
Proper citation: Mouse Genome Informatics (MGI) (RRID:SCR_006460) Copy
http://tardis.nibio.go.jp/homstrad/
A curated database of structure-based alignments for homologous protein families. All known protein structure are clustered into homologous families (i.e., common ancestry), and the sequences of representative members of each family are aligned on the basis of their 3D structures using the programs MNYFIT, STAMP and COMPARER. These structure-based alignments are annotated with JOY and examined individually.
Proper citation: HOMSTRAD - Homologous Structure Alignment Database (RRID:SCR_006544) Copy
http://bioinformatics.intec.ugent.be/magic/
Web based interface for exploring and analyzing a comprehensive maize-specific cross-platform expression compendium. This compendium was constructed by collecting, homogenizing and formally annotating publicly available microarrays from Gene Expression Omnibus (GEO), and ArrayExpress.
Proper citation: Magic (RRID:SCR_006406) Copy
https://www.ncbi.nlm.nih.gov/geo/
THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022.
Proper citation: NCBI Epigenomics (RRID:SCR_006151) Copy
http://www.mybiosoftware.com/seaview-4-2-12-sequence-alignment-phylogenetic-tree-building.html
Graphical user interface for multiple sequence alignment and molecular phylogeny. SeaView also generates phylogenetic trees.
Proper citation: SeaView (RRID:SCR_015059) Copy
https://sourceforge.net/projects/giira/
Gene prediction method that identifies potential coding regions based on the mapping of reads from an RNA-Seq experiment.
Proper citation: GIIRA (RRID:SCR_015507) Copy
https://github.com/johnlees/seer
Sequence element enrichment analysis tool to perform pan-genome-wide association studies in bacteria.
Proper citation: SEER (RRID:SCR_015499) Copy
https://github.com/cmayer/BaitFisher-package
Software toolkit for multispecies target DNA enrichment probe design. It consists of two programs: BaitFisher and BaitFilter, which are designed to construct hybrid enrichment baits for multiple sequence alignments or annotated features in multiple sequence alignments.
Proper citation: Baitfisher (RRID:SCR_015985) Copy
Software for semantic chemical editing, visualization, and analysis. It is designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
Proper citation: Avogadro (RRID:SCR_015983) Copy
https://github.com/sanger-pathogens/Bio-Tradis
Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools.
Proper citation: Bio-tradis (RRID:SCR_015993) Copy
https://github.com/katholt/srst2
Software that is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes.
Proper citation: Short Read Sequence Typing for Bacterial Pathogens (RRID:SCR_015870) Copy
http://standage.github.io/AEGeAn
Software toolkit for the analysis and evaluation of genome annotations. The toolkit includes a variety of analysis programs, e.g. for comparing distinct sets of gene structure annotations (ParsEval), computation of gene loci (LocusPocus) and more.
Proper citation: Aegean (RRID:SCR_015965) Copy
https://github.com/EvolBioInf/andi
Software tool for rapidly computing and estimating evolutionary distance between closely related genomes. Because andi does not compute full alignments it scales even up to thousands of bacterial genomes.
Proper citation: andi (RRID:SCR_015971) Copy
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