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.  This resource was the basis of a proposal funded by the University of Washington Student Technology Fee.  Database and software servers have been purchased and installed at the Health Sciences Library and Department of Pathobiology (School of Public Health and Community Medicine), University of Washington. Software and site-licenses have been purchased to provide students access to comprehensive analytical and database management software. Four bioinformatics workstations have been established in the Health Sciences Library and in the Department of Pathobiology for software development and bioinformatics training.  Sequence analysis software is currently being developed for use through a Web browser.  Formal training in Bioinformatics is available through the graduate level course, PABIO 536 "Bioinformatics and Gene Sequence Analysis" (Instructor - T. Rose )

The University of Washington BioCommons	Quick Links: ENTREZ, BLAST, Entrez Gene, OMIM, RefSeq, SwissProt, UniGene
DNA Analysis Tools	Protein Analysis Tools
Codon Usage Codon Usage - Cusp (Pasteur) Codon Usage (SMS) Codon Usage-graphical (GCUA) Genetic Code- Standard(NIH) Gene Finder Analysis GeneFinder (SoftBerry) GeneFinder (BCM) SeqHelp (UW-restricted) Pattern/Sequence analysis Motif Search – (Pasteur) Restriction Site Analysis (BCM) 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) Reverse Complement DNA Sequence (Invert) Reverse Complement (BCM) Reverse Complement (SMS) Sequence Alignment 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 (UW-restricted) Multiple Alignment via ClustalW (Pasteur) Multiple Alignment via ClustalW (CH.EmbNet) Align transcript with genome sequence (Splign; NCBI) Similarity/Homology Analysis BLAST (UW-restricted) 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 (UW-restricted) Translate DNA (EMBOSS) Translate DNA (ExPASy) Translate DNA (UMass) Translate DNA and ORF analysis (Colorado State) ORF Finder (NCBI) ORF Analysis (Colorado State) ORF Analysis (UMass Best ORF (SoftBerry)	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) Statistical Analysis of Protein Sequences (ISREC) Pattern/Sequence Analysis AminoTrack – mutation analysis of multiple alignment (SBRI) Antigenicity Predictions (ExPASy) Glycosylation sites (N-linked) (CBS) Glycosylation sites (O-linked) (CBS) Motif Search – (Pasteur) Pattern Search - PatScan 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 Region and Orientation - BCM Transmembrane Helices- CBS Sequence Alignment Pairwise Alignment (EMBL) Pairwise Alignment (MTU) Pairwise Alignment (IGH) Pairwise Alignment via BLAST (NCBI) Protein Alignment with Gene Sequence (EMBL) Multiple Sequence Alignment Tools - BCM Multiple Sequence Graphing Tool (Graph Align) Sequence Logos - Displaying consensus sequences Web Logo (Berkeley) Alignment output tool (Boxshade) - ISREC Align transcript with genome sequence (Splign; NCBI) Similarity/Homology Analysis Phylogeny Analysis - PHYLIP Phylogeny Analysis - WebPhylip (NUS) Phylogeny Analysis - PhyloBLAST - GSC Phylogeny Analysis - WebPhylip (Pasteur) Phylogenetic Tree Printer -Phylodendron (IUBIO) Structure (Secondary) Analysis Secondary Structure (Biology Workbench)  - NCSA Secondary Structure - BCM search launcher Structure (Tertiary) Analysis ConSurf - Identification of Functional Regions by Surface Mapping Molecular Modelling (NCBI) Protein Explorer (U of M) Protein Structure Prediction (PSIPRED) 3D-PSSM Structure Prediction (ICS) Structure Prediction (UCLA-DOE) 123D Structure Threading PHD Threader (Heidelberg)

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) BCM - Analysis Tools BioExchange Bioinformatic Tools and Databases Descriptions (BRC) Bioinformatics.Org - On Line Software Bioinformatik EMBL - Database Searching, Browsing and Analysis Tools EMBOSS suite of sequence analysis tools Expasy – Proteomic Tools CBS - Center for Biological Sequence Analysis Prediction Servers 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) 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

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

Software and site development by Jonathan Ryan (Pathobiology), Cliff Olmsted (Electrical Engineering), James Wallace & Emily Schultz (Molecular Biotechnology), Jonathan Schaefer (Molecular & Cellular Biology Graduate Program), Philip Pantoja, and Dennis Kowalik.

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

Last Modified 4/6/08 by E. Cadag, T.Rose, J.Ryan.

Copyright © 1999 Department of Pathobiology, University of Washington