Biological Information Resource – University of Washington (http://courses.washington.edu/bioinfo)

The Biological Information Resource is being developed to provide general access for students at the University of Washington to centralized biological sequence databases and software programs to interact with these databases.  Formal training in Bioinformatics is available from the Interdisciplinary Ph.D. Program in Pathobiology, the Department of Biomedical Health Informatics and the Institute of Public Health Genetics, University of Washington, through the graduate level course, PABIO/MEBI/PHG 536 "Bioinformatics and Gene Sequence Analysis" (Instructor - T. Rose )

The University of Washington BioCommons	Quick Links: ENTREZ, BLAST, Entrez Gene, OMIM, RefSeq, SwissProt, UniGene, Ensembl
DNA Analysis Tools	Protein Analysis Tools
File Conversion ReadSeq Sequence conversion (Seqret; EMBOSS) Codon Usage Codon Usage - Cusp (Pasteur) Codon Usage (SMS) Codon Usage-graphical (GCUA) Genetic Code- Standard(NIH) Gene Finder Analysis GeneFinder (SoftBerry) GeneFinder (BCM) Pattern/Sequence analysis Nucleotide Motif Search - Fuzznuc (EMBOSS) Web Cutter (Heiman) Restriction Site Map -ReMap (EMBOSS) Restriction Enzyme Mapping (UMass) Tandem Repeat Finder - MS Primer Analysis/Selection Degenerate Primer Design (CODEHOP) Interactive Degenerate Primer Design (iCODEHOP) Primer Design and Analysis Tools (IDT) Oligonucleotide Properties Calculator (NWU) Primer 3- Primer Selection Software (WIBR) Primo Pro - Primer Selection Software (UTSW) ePrimer3 – (Pasteur) Primer-BLAST (NCBI) Reverse Complement DNA Sequence (Invert) Sequence conversion (Seqret; EMBOSS) Reverse Complement (SMS) Sequence Alignment CodonAlign – nucleotide to codons (LANL) Consensus Maker (LANL) Pairwise Alignment (MTU) Pairwise Alignment (EMBL) Pairwise Alignment (IGH) Pairwise Alignment via BLAST (NCBI) Pairwise Alignment via Dot Matrix(Colorado State) Merge two DNA sequences (Pasteur) Multiple Alignment via ClustalW (Pasteur) Multiple Alignment via ClustalW (CH.EmbNet) Align transcript with genome sequence (Splign; NCBI) Similarity/Homology Analysis BLAST (NCBI) Impala Searcher to search a sequence vs Blocks-FHCRC PHYLIP - Phylogeny Analysis Structure Analysis DNA mfold analysis (RPI) RNA mfold analysis - RPI Translate DNA/Open Reading Frame Analysis Translate DNA (EMBOSS) Translate DNA (ExPASy) Translate DNA (UMass) Translate DNA and ORF analysis (Colorado State) Translate 6 ORFs with DNA (Sixpack; EMBOSS) ORF Finder (NCBI) ORF Analysis (UMass Best ORF (SoftBerry) Gene Feature Predictions Splice-site predictions (BDGP) Transcription factor binding site prediction (CBRC) Promoter prediction (BDGP)	Amino Acid Information and Composition Amino Acid Explorer (NCBI) Amino Acid Structures and Properties (U.Berlin) Genetic Code- Standard(NIH) Amino Acid Composition - MIT Helical Wheel Draw (U.Ottawa) Hydropathy Analysis - UCSD Isoelectric Point (pI) - ExPASy Peptide Guide - PG Peptide Statistics Tool (UMass) Peptide Statistics (Pepstat; EMBOSS) Pattern/Sequence Analysis AminoTrack – mutation analysis of multiple alignment (SBRI) Antigenicity Predictions (ExPASy) Eukaryotic Linear Protein Motif resource (ELM) Glycosylation sites (N-linked) (CBS) Glycosylation sites (O-linked) (CBS) Motif Search – (Pasteur) Protein Motif search – FuzzPro (EMBOSS) Phosphorylation Prediction (EMBL) Post-translational Modifications Prediction (ExPASy) PSSM viewer (NCBI) Protease Cleavage Prediction (ExPASy) Profile Scan Server - ISREC Protein Sorting Signals (U.Tokyo) Reverse Translate Protein into DNA-Colorado State Signal Sequence Prediction - CBS Signal Sequence Cleavage (UMass) Transmembrane Helices- CBS Transmembrane Topology (UCL) Sequence Alignment CodonAlign – nucleotide to codons (LANL) Pairwise Alignment (EMBL) Pairwise Alignment (IGH) Pairwise Alignment via BLAST (NCBI) Protein Alignment with Gene Sequence (EMBL) Multiple Alignment via COBALT (NCBI) Multiple Alignment via Muscle (EMBL-EBI) Multiple Alignment via ClustalW (Pasteur) Multiple Alignment via ClustalW (CH.EmbNet) Multiple Alignment via ClustalW (EMBL-EBI) Multiple Alignment via ClustalW (PIR) Sequence Logos - Displaying consensus sequences SeqPublish-publishable alignments(SeqPublishLANL) Web Logo (Berkeley) Alignment output tool (Boxshade) - ISREC Align transcript with genome sequence (Splign; NCBI) Similarity/Homology Analysis Phylogeny Analysis - PHYLIP Phylogeny Analysis – DNA phylogeny methods (Pasteur) Phylogeny Analysis – Protein phylogeny methods (Pasteur) Phylogenetic Tree Printer -Phylodendron (IUBIO) Phylogeny.fr – Web-based tool set (LIRMM) PhyML – generates ML trees (LANL) Structure (Secondary) Analysis Secondary Structure (Biology Workbench)  - NCSA PSIPRED – secondary structure (UCL) Structure (Tertiary) Analysis ConSurf - Identification of Functional Regions by Surface Mapping Protein structure search with a structure (Dali) Molecular Modelling (NCBI) Protein Explorer (U of M) Protein Structure Prediction (PSIPRED) Phyre2 -Structure Prediction (ICS) Structure Prediction (UCLA-DOE) 123D Structure Threading PHD Threader (Heidelberg) Gen Threader (UCL)

Database Search Tools

Sequence Analysis Sites

BLAST - NCBI BLAST - ExPasy BCM - Search Launcher BLAST - Sanger (Genome projects) Electronic PCR for STS genomic map positions Entrez Browser (Genbank +Genpep+Medline) Genome Machine - Graphical Interface to OMIM (UW) LocusLink Interface to curated sequences/genetic loci (NCBI) Protein Family Classification Search ScanProsite - ExPASy

ABI - On-Line Analysis Tools BioCatalog - Software Directory (EBI) BioExchange Bioinformatics.Org - On Line Software Bioinformatik EMBL - Database Searching, Browsing and Analysis Tools EMBOSS – Sequence analysis tools Expasy – Proteomic Tools CBS - Center for Biological Sequence Analysis Prediction Servers Bioinformatic tools (IGC) Protein Sequence Homology: Identity, Search and Analysis (CMSMBR) Sequence Analysis Tools (NIH) Sequence Manipulation Site · BioEdit - Multi-featured Analysis Package (Highly Recommended) Free Download Mega 2.1 - Multi-featured Phylogenetic Analysis Package (Free Download) GeneDoc - Multiple Sequence Alignment Editor, Analyzer and Shader (Free Download)

Databases

Protein and Protein Families

Blocks WWW Server for Protein Analysis, (FHCRC) Conserved Domain Database (NCBI) dbSNP - Single Nucleotide Polymorphisms (NCBI) dbEST - Expressed Sequence Tags (NCBI) dbSTS - Sequence Tagged Sites (NCBI) GenBank (NCBI) Gene Expression Profiles (GEO) Genome DataBase (GDB) HapMap Project Human Gene Mutation Database (HGMD) MMDB - Molecular Modeling (NCBI) OMIM - Online Mendelian Inheritance in Man (NCBI) PopSet - Population Study data sets (NCBI) Prosite - Protein Families and Domains(ExPASy) Protein Data Bank (PDB) RefSeq - mRNA Reference Sequences (NCBI) Sexually Transmitted Disease Sequence Database (Los Alamos) Swiss Prot - Annotated Proteins (ExPASy) UNIGENE - gene-based view of Genbank sequences

Expansion of Gene Families using CODEHOPs Building Gene Families (Science Article) Integrated Resource of Protein Families (Interpro) Nuclear Receptor Database Peptidase Data Base (Merops) Protein Family List and Links (ProWeb, FHCRC) Protein Information Resource (NBRF) ProWeb - Protein Family Classification System G-Protein Coupled Receptor Information

Genomes

Taxonomy

Ensembl genome browser Genome-Specific Resources (NCBI) SEQUENCE OF THE HUMAN GENOME (Science issue)**** SEQUENCE OF THE HUMAN GENOME (Nature issue)**** THE HUMAN GENOME - online resources (NCBI)**** COMPLETED GENOMES (Entrez/NCBI) Cancer Genome Anatomy Project Genome Landmarks (Science) Human Gene Map (NCBI) Human Genome Browser (UCSC) Human Genome Guide (NCBI) Human Genome Project Guide (NCBI) Human Genome Sequencing (NCBI) Human/Mouse Homology Maps (NCBI) Viral Genomes Resource (NCBI) Retroviruses (NCBI) Herpesviruses

Taxonomy Browser (NCBI) Universal Virus Database (ICTVdB)

Molecular Biology and Genetics Links

Bioinformatics Readings, Information and Courses

Amos Bairoch's WWW links to Biological Macromolecules Molecular Biology and Genetics Resources (Software, Databases, Links) UW HealthLinks National Center for Biotechnology Information (NCBI) Molecular Biology CyberLab (U. Illinois)

Bioinformatics at the University of Washington Bioinformatics Tools Tutorial - 2Can Blossum 62 Amino Acid Substitution Matrix Reference (Henikoff and Henikoff) Primer on Molecular Genetics - Human Genome Project (Department of Energy) Genes and Diseases (NCBI) Genomics and its Impact on Medicine and Society (HGP) SADR - Web based course on sequence analysis (U. Bielefeld) The Human Genome Project - To Know Ourselves (HGP) "Bioinformatics and Gene Sequence Analysis" PABIO536 (UW) Master's Program in Bioinformatics (Swiss Inst. Bioinformatics) Public Health Genetics 581 "Genetic Services and Bioinformatics (UW) Nutrition and Gene Expression - Bioinformatics NWABR: Bioinformatics and Sequence Variation

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For questions and information concerning this site, please contact Dr. Timothy M. Rose, Dept. Pediatrics, trose@u.washington.edu.  Rose Lab Web Site

Last Modified 4/6/13 by T.Rose.

Copyright © 1999 Department of Pediatrics, University of Washington