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Understanding Bioinformatics book website
- Molecular Biology/Genetics/Genomics Tutorials
- Unix/Linux/Programming Tutorials
- Bioinformatics Online Books/Tutorials
- Bioinformatics Tools: Web Server
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NCBI: National Center for Biotechnology Information (BLAST, Entrez, GenBank,
)
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NCBI Sequence Analysis Tools
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BLAST: Basic Local Alignment Search Tool @ NCBI
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ExPASy Bioinformatics Resource Portal
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The European Bioinformatics Institute (EBI) Tools
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Max-Planck Institute Bioinformatics Toolkit
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Software tools @ LANL HIV database website
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Service @ DTU Health Tech: Bioinformatics software
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Software Downloads @ DTU Bioinformatics
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GenomeNet @ Kyoto University Bioinformatics Center: Bioinformatics Tools
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GenScript: Bioinformatics Tools
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ISGA: Integrative Services for Genomic Analysis
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BROAD Institute Software list
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JGI (Joint Genome Institute) Data & Tools (including IMG, GOLD, etc.)
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Bioinformatics Software at Wageningen University Bioinformatics group (including Phylip programs)
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Selected EMBOSS tools for sequence analysis at EMBL-EBI
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EMBOSS Explorer at Wageningen University Bioinformatics group (including Phylip programs)
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EMBOSS Explorer at University of Tronto
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EMBOSS Explorer at National Research Institute for Agriculture, Food and Environment (INRAE), France
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EMBOSS Explorer at EMBNet Columbia
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EMBOSS Explorer at Universidad Complutense Madrid
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List of EMBOSS servers @ sourceforge.net
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Cytoscape
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QIIME 2: Quantitative Insights Into Microbial Ecology
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Galaxy: an open, web-based platform for data intensive biomedical research
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CyVerse (formerly iPlant Collaborative): a cyberinfrastructure for life scientists to handle huge datasets and complex analyses
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RDP CLassifier (a naive Bayesian classifier for bacterial and archaeal 16S rRNA sequences, fungal LSU and fungal ITS sequences)
[Originally used in RDP database, which is no longer available]
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HMMER: biosequence analysis using profile hidden Markov models
[used with Pfam and other profile HMM databases]
- Bioinformatics/Molecular Evolution Tools: Standalone Package (free)
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Multiple Alignment, Alignment Editors, and Phylogenetic Reconstruction/Visualization
- Sequence/alignment format conversion
- Simple Open Reading Frame (ORF) finder and translation
- Dotplot
- LALIGN, PRSS, FASTA, SSEARCH
- Databases
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NCBI Databases and Global Cross-database Search (aka Entrez; list of databases including PubMed, Genbank)
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UniProt: Universal Protein Resource (including Swiss-Prot)
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HAMAP: High-quality Automated and Manual Annotation of Proteins
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PIR: Intergrated Protein Informatics Resource for Genomic, Proteomic and Systems Biology Research
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PDB: Protein Data Bank
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SCOP 2: Structural Classification of Proteins
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SCOP2 prototype: Structural Classification of Proteins 2 (the beta version, use the version above)
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SCOP (1.75): Structural Classification of Proteins (the original SCOP, no longer updated)
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CATH/Gene3D: Protein Structural Classification
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InterPro: a database of protein families (including Pfam)
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Rfam: a collection of RNA sequence families of structural RNAs @ EBI
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Dfam: a database of repetitive DNA based on profile hidden Markov models
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TreeFam: a database of animal gene trees
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SUPERFAMILY HMM library and genome assignments server
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PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System
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SMART: Simple Modular Architecture Research Tool
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PROSITE: Database of protein domains, families and functional sites
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KEGG: Kyoto Encyclopedia of Genes and Genomes
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BioCyc Database Collection (including BioCyc, EcoCyc, MetaCyc, HumanCyc, BsubCyc, and Pathway Tools)
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Gene Ontology
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SILVA comprehensive ribosomal RNA database
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The greengenes: 16S rRNA gene database
- Genome Databases and Genome Browsers
- Genome Databases (organism specific)
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Flybase: A Database of Drosophila Genes & Genomes
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Sequenced Arthropod Genomes from i5k initiavive
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Ag100Pest Initiative from i5k initiavive
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Hymenoptera Genome Database (including BeeBase, NasoniaBase, Ant Genomes)
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InsectBase (integrated genome and transcriptome resources of insects)
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VectorBase (including Anopheles, Aedes, Ixodes, Culex, Pediculus, Rhodnius, Glossina)
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AphidBase: The Aphid Genome Database
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TAIR: The Arabidopsis Information Resource
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MaizeGDB: Maize Genetics and Genomics Database
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EnsemblPlants
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Phytozome: The Plant Genomics Resource at JGI
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Plant GARDEN (Genome And Resource Database Entry)
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Fungal Genome Initiative (FGI) at BROAD Institute
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MycoCosm: The Fungal Genomics Resource at JGI
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Saccharomyces Genome Database (SGD)
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Candida Genome Database (CGD)
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Fungal Genome Collection (our own! But currently not updated)
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FungiDB
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VEuPathDB: Eukaryotic Pathogen Database Resources
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WormBase: The database for C. elegans and related nematodes
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dictyBase: The Dictyostelid Genome Database
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Earth Biogenome Project Genome Database
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NIH Human Microbiome Project (HMP)
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Integrated Microbial Genomes & Microbiomes at JGI
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ViralZone
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GISAID (including genomic information of Influenza viruses, coronaviruses, monkeypox virus, and RSV)
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Virus-Host DB at GenomeNet
- Gene/genome/functional annotations
- Scientific calculator (with full precision)
- PDF converter
- @ UNL
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