¶ Additional Resources
¶ Analysis Resources
¶ Eukaryote Resources
BahlerLab Tools for analyzing S. pombe genetics and genetic regulation- BLAT Search Genome Quickly find sequences of 95% and greater similarity of length 25 bases or more
- COXPRESdb Database providing coexpression information for 11 animal species
- EpiGenie Search out and compile a list of the best free tools and databases that epigenetics researchers
- EuPathDB Eukaryotic pathogenes database
- GenAtlas Scientific and clinical digests on genes and diseases
- GeneCards The Human Gene Database
- Human Brain Map Multimodal atlas of the human brain, integrating anatomic and genomic information
- HPM Resource that reorganizes mass spectrometry-based proteomics data
- NIH LINCS Network-based catalog of gene expression and other cellular processes
- OMIM Comprehensive, authoritative compendium of human genes and genetic phenotypes
- X2K Infers upstream regulatory networks from signatures of differentially expressed genes
¶ Fungi Resources
- FungiDB Fungus database
- FUNGIpath Orthologous proteins in fungal genomes database
- Saccharomyces Genome Database Comprehensive integrated biological information for the budding yeast S. cerevisiae
¶ Plant Resources
- Arabidopsis Information Resource (TAIR) database of genetic and molecular biology data for A. thaliana
- AraNet Functional gene network for Arabidopsis thaliana
- ATTED-II Coexpression database for plants to discover relationships of unknown genes within a species
- Diurnal Provides convenient access to circadian and diurnal genome-wide gene expression data
- eFP Schematic representation of data for Arabidopsis seedlings
- Phylogenes Pre-computed phylogenetic trees of gene families alongside experimental gene function data
- qTeller for MaizeGDB Comparative RNA-seq expression platform for Zea mays genome
¶ Experimental Planning Resources
- ABCDdb ABCD database is a manually curated depository of sequenced antibodies
- ApE Tool that allows information and editing of plasmids, as well as tools for data visualization
- Gene Infinity Online place to find information and resources needed in molecular biology and biochemistry
- NEBcutter Take DNA sequence and find the large, open reading frames using the E.coli genetic code
- Primer3Plus Pick primers from a DNA sequence
- Primer-BLAST A tool for finding specific primers
¶ Galaxy Resources
¶ General Resources
- BioNumbers Enable you to find in one minute any useful molecular biology number
- BioPortal Comprehensive repository of biomedical ontologies
- EMBL-EBI Services and tools, perform basic research and provide professional training in bioinformatics
- EZBioCloud ChunLab's public data and analytics portal
- FAIRsharing A curated, informative and educational resource on data and metadata standards
- GenomeNet Database Database of integrated genomes
- ICTV Charged with the task of developing, refining, and maintaining a universal virus taxonomy
- MassBank Official database of the Mass Spectrometry Society of Japan
- NAR Database Summary Category list
- NCBI All Resources
- NCBI Search engine
- Omictools Online community & aggregating resource of bioinformatic software, platforms & tools
- Online Bioinformatics Resources Collection Contains annotations and links for 2449 bioinformatics databases and software tools
- Online Structure Alignment Resources Web page provided a list of various tools and resources used in online structure alignments
- Phage Directory List of phage bioinformatics tools and resources
- Quest for Orthologs Provides a list of existing orthology databases
- re3data Global registry of research data repositories that covers research data repositories
- RTH Analysis of the mammalian genome for non-coding RNAs in relation to (inflammatory) diseases
- SAT Web page describing various structural alignment tools and resources
- Scinapse Free academic search engine
- UniProt Comprehensive resource for protein sequence and annotation data
- VARIDT Variability of drug transporter database
- Wiki bio databases Wiki page that list biological databases
¶ Homology
- JGI-IMG - Phylogeny Assess phylogenetic composition of a metagenome sample based
- Genoscope Microscope Phyloprofile Allows to search for common OR specific genes between genomes
¶ Protein Analysis Resources
- Binding MOAD Subset of the Protein Data Bank (PDB), containing every high-quality example of ligand-protein binding
- BioInfo3D A suite of freely available web services for protein structural analysis
- CyBase The database of cyclic proteins
- ExPASy Proteomics Bioinformatic resources for proteomics
- MetOSite Compilation of oxidized methionine, post-translational modifications
- Protein Structure Prediction Center Advance the methods of identifying protein structure from sequence
- SFLD Hierarchical classification of enzymes that relates specific sequence-structure features