BIOS 477/877 Bioinformatics and Molecular Evolution (3 credits)

[Last updated: March 22, 2025]

Links:

• Understanding Bioinformatics book website


• Molecular Biology/Genetics/Genomics Tutorials


• Unix/Linux/Programming Tutorials


• Bioinformatics Online Books/Tutorials
• "Sequence-Evolution-Function: Computational Approaches in Comparative Genomics"
  by Koonin and Galperin
• NCBI Tutorials (BLAST, Amino Acid Explorer, etc.)
• NCBI Help Manual (BLAST, Entrez, PubMed, etc.)
• NCBI YouTube Channel (tutorials for many NCBI tools including BLAST/E-values)
• NCBI Documentation (online manuals, handbooks, fact sheets, and FAQs)
  
• EMBL-EBI: On-demand training
• National Human Genome Research Institute: Educational Resources, Bioinformatics
• Max Planck Institute Online Lectures on Bioinformatics
• Genetics Learning Resources at the Jackson Laboratory
• Teaching with Genome Blowser from UCSC Genome Browser
• UCSC Genome Blowser tutorials
• PLoS Computational Biology Collections
• Bielefeld University BiBiServ Bioinformatics Courses
• Bates Bioinformatics Tutorial
• Bioinformatics Crash Course @ UCSD/UBIC
• Bioinformatics and Homology Modeling: A Student-Tested Tutorial for Beginners
• Bioinformatics, Sequence and Structural Alignment


• Bioinformatics Tools: Web Server
  • NCBI: National Center for Biotechnology Information (BLAST, Entrez, GenBank, …)
  • NCBI Sequence Analysis Tools
  • BLAST: Basic Local Alignment Search Tool @ NCBI
  • ExPASy Bioinformatics Resource Portal
  • The European Bioinformatics Institute (EBI) Tools
  • Max-Planck Institute Bioinformatics Toolkit (HHblits, HHpred, MMseqs2, DIAMOND-DeepClust, etc.)
  • Software tools @ LANL HIV database website
  • Service @ DTU Health Tech: Bioinformatics software
  • Software Downloads @ DTU Bioinformatics
  • GenomeNet @ Kyoto University Bioinformatics Center: Bioinformatics Tools
  • GenScript: Bioinformatics Tools
  • ISGA: Integrative Services for Genomic Analysis
  • BROAD Institute Software list
  • JGI (Joint Genome Institute) Data & Tools (including IMG, GOLD, etc.)
  • Bioinformatics Software at Wageningen University Bioinformatics group (including Phylip programs)
  • Selected EMBOSS tools for sequence analysis at EMBL-EBI
  • EMBOSS Explorer at Wageningen University Bioinformatics group (including Phylip programs)
  • EMBOSS Explorer at EMBNet Columbia
  • EMBOSS Explorer at Universidad Complutense Madrid
  • List of EMBOSS servers @ sourceforge.net
  • Sequence Maniplation Suite
  • Cytoscape
  • QIIME 2: Quantitative Insights Into Microbial Ecology
  • Galaxy: an open, web-based platform for data intensive biomedical research
  • CyVerse (formerly iPlant Collaborative): a cyberinfrastructure for life scientists to handle huge datasets and complex analyses
  • 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]
  • HMMER: biosequence analysis using profile hidden Markov models
    [used with InterPro/Pfam and other profile HMM databases]
  
  
• Bioinformatics/Molecular Evolution Tools: Standalone Package (free)
  • Unipro UGENE
  • MEGA: Molecular Evolutionary Genetics Analysis
  • DAMBE: Data Analysis and Molecular Biology and Evolution
  • Sequence Analysis by Will Gilbert at informagen.com
  • UTOPIA Protein Analysis Suite and UTOPIA Documents
  
  
• Multiple Alignment, Alignment Editors, and Phylogenetic Reconstruction/Visualization
  
  
• Sequence/alignment format conversion
  • EMBOSS Seqret @ EBI (can convert ABI tracefile, BAM, FASTQ, GFF3, etc.)
  • Readseq 2.1.30 @ MABL
  • Readseq @ mafft.cbrc.jp
  • Format Converter @ lanl.gov (can convert Genbank to GFF3)
  • Sequence conversion @ bugaco.com (can convert ABI tracefile, FASTQ, etc.)
  • Readseq @ Kitasato-U
  
  
• Simple Open Reading Frame (ORF) finder and translation
  • Translation tool @ ExPASy
  • EMBOSS translation programs:
    • Transeq (outputs translation of each frame individually)
    • Sixpack (outputs the three forward and three reverse strands translation along the nucleotide sequence)
  • Translate @ Sequence Maniplation Suite
  • ORF Finder @ NCBI
  
  
• Dotplot
  • Dotlet JS beta - Javascript based Dotlet
  • Dotlet - MyHits - SIB (uses old version of Java, not accessible from UNL domain)
  • YASS: genome similarity search tool
  • D-Genies - Dot plot large Genomes in an interactive, efficient and Simple way (online and standalone)
  • EMBOSS/dotmatcher (see also the above section for links to other EMBOSS websites)
    • from Wageningen University
    • from EMBL-EBI
  • EMBOSS/dottup @ EMBL-EBI
  • Dotter (part of SeqTools)
  • JDotter: Java Dot Plot Alignments
  • JDotter: Java Dot Plot alignments @ University of Victoria
  • FlexiDot: Customizable, ambiguity-aware dotplot suite implemented in Python


• LALIGN, PRSS, FASTA, SSEARCH
  • LALIGN server @ EBI
  • FASTA Sequence Comparison server @ U Virginia (Website by Bill Pearson, the original author of FASTA, includes LALIGN, PRSS, FASTA,SSEARCH and more)
  • FASTA/SSEARCH/GGSEARCH/GLSEARCH protein similarity search @ EBI
  • FASTA Search @ Kyoto University Bioinformatics Center


• Databases
  • NCBI Databases and Global Cross-database Search (aka Entrez; list of databases including PubMed, Genbank)
  • UniProt: Universal Protein Resource (including Swiss-Prot)
  • HAMAP: High-quality Automated and Manual Annotation of Proteins
  • PIR: Intergrated Protein Informatics Resource for Genomic, Proteomic and Systems Biology Research
  • PDB: Protein Data Bank
  • SCOP 2: Structural Classification of Proteins
  • CATH/Gene3D: Protein Structural Classification
  • InterPro: a database of protein families (including Pfam)
  • Rfam: a collection of RNA sequence families of structural RNAs @ EBI
  • Dfam: a database of repetitive DNA based on profile hidden Markov models
  • TreeFam: a database of animal gene trees
  • SUPERFAMILY 2: Structural and functional annotation of proteins and genomes (for legacy version 1.75, see below)
  • SUPERFAMILY 1.75
  • PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System
  • SMART: Simple Modular Architecture Research Tool
  • PROSITE: Database of protein domains, families and functional sites
  • KEGG: Kyoto Encyclopedia of Genes and Genomes
  • BioCyc Database Collection (including BioCyc, EcoCyc, MetaCyc, HumanCyc, BsubCyc, and Pathway Tools)
  • Gene Ontology
  • SILVA comprehensive ribosomal RNA database
  • Greengenes 2: unified 16S rRNA gene database
  
  
• Genome Databases and Genome Browsers
  • NCBI Genome
  • Ensemble genome databases
  • UCSC Genome Browser Gateway
  • JGI Genome Portal (including Mycocosm for Fungal Genomics, IMG for Microbial Genomics, IMG/M for Metagenomics, Phytozome for plant genomics, and more)
  • JGI Genomes OnLine Database (GOLD)
  • BROAD Institute: Data
  
  
• Genome Databases (organism specific)
  • Flybase: A Database of Drosophila Genes & Genomes
  • Sequenced Arthropod Genomes from i5k initiavive
  • Ag100Pest Initiative from i5k initiavive
  • Hymenoptera Genome Database (including BeeBase, NasoniaBase, Ant Genomes)
  • InsectBase (integrated genome and transcriptome resources of insects)
  • VectorBase (including Anopheles, Aedes, Ixodes, Culex, Pediculus, Rhodnius, Glossina)
  • AphidBase: The Aphid Genome Database
  • TAIR: The Arabidopsis Information Resource
  • MaizeGDB: Maize Genetics and Genomics Database
  • Phytozome: The Plant Genomics Resource at JGI
  • Plant GARDEN (Genome And Resource Database Entry)
  • Fungal Genome Initiative (FGI) at BROAD Institute
  • MycoCosm: The Fungal Genomics Resource at JGI
  • Saccharomyces Genome Database (SGD)
  • Candida Genome Database (CGD)
  • Fungal Genome Collection (our own! But currently not updated)
  • FungiDB
  • VEuPathDB: Eukaryotic Pathogen Database Resources
  • WormBase: The database for C. elegans and related nematodes
  • dictyBase: The Dictyostelid Genome Database
  • Earth Biogenome Project Genome Database
  • NIH Human Microbiome Project (HMP)
  • Integrated Microbial Genomes & Microbiomes at JGI
  • ViralZone
  • GISAID (including genomic information of Influenza viruses, coronaviruses, monkeypox virus, and RSV)
  • Virus-Host DB at GenomeNet
  
  
• Gene/genome/functional annotations
  • Database for Annotation, Visualization and Integrated Discovery (DAVID)
  • The National Centor for Toxicological Research (NCTR): Bioinformatics Tools
  • The SEED
  • MG-RAST: Metagenomics RAST
  • MEGAN - MEtaGenome ANalyzer and related resources @ University of Tübingen
  • Integrated Microbial Genomes & Microbiomes at JGI
  • CyVerse (formerly iPlant Collaborative): a cyberinfrastructure for life scientists to handle huge datasets and complex analyses
  • STRING: protein-protein interaction network database
  • KBase (DOE Systems Biology Knowledgebase)
  • BV-BRC (Bacterial and Viral Bioinformatics Resource Center)
    [combines the bacterial system PATRIC and the viral system IRD/ViPR, funded by NIAID]
  
  
• Scientific calculator (with full precision)
  • Online Calculators
  • Scientific Calculator at MathisFun.com
  • Web2.0 Calc (online, precistion is not as good as others)
  • PCalc for Mac OS X (standalone software, also for iPhone/iPad)
  • Calculator @ Google (by searching "calculator" in Google, you can call up a calculator)
  
  
• PDF converter
  • Smallpdf: online PDF converter/compressor
  
  
• @ UNL
  • UNL Home
  • My UNL (Canvas)
  • UNL Zoom
  • UNL Holland Computing Center
  • UNL Bioinformatics Core Research Facility
  • Moriyama Lab Home Page
  
  
  • List of bioinformatics and related courses at UNL