Biological Information Resource v2.5, University of Washington

Biological Information Resource – University of Washington

The Biological Information Resource provides general access for students at the University of Washington to centralized biological sequence databases and software programs to interact with these databases.

	Quick Links: PubMed, BLAST, NCBI-Gene, OMIM, RefSeq, SwissProt, UniGene, Ensembl
DNA Analysis Tools	Protein Analysis Tools
Genetic Codes IUPAC codes File Conversion ReadSeq Codon Usage Codon Statistics (Virology.ca) Codon Usage - Cusp (Pasteur) Codon Usage (SMS) Codon Usage-graphical (GCUA) Genetic Code- Standard(NIH) Gene Finder Analysis GeneFinder (SoftBerry) Pattern/Sequence analysis Nucleotide Motif Search - Fuzznuc (EMBOSS) Restriction Site Map -ReMap (EMBOSS) Restriction Enzyme Mapping (UMass) Tandem Repeat Finder - MS Sequence Searcher – motif finder (Virology.ca) Primer Analysis/Selection Degenerate Primer Design (CODEHOP) old Degenerate Primer Design (J-CODEHOP) new Primer Design and Analysis Tools (IDT) Oligonucleotide Properties Calculator (NWU) Primer 3- Primer Selection Software (WIBR) Primo Pro - Primer Selection Software (UTSW) Primer-BLAST (NCBI) Reverse Complement DNA Sequence (Invert) Reverse Complement (SMS) Sequence Alignment Align transcript with genome sequence (Splign; NCBI) Base-By-Base whole genome pairwise/alignment editor (Virology.ca) CodonAlign – nucleotide to codons (LANL) Consensus Maker (LANL) NAP nucleotide-amino acid alignment (Virology.ca) Pairwise Alignment (EMBL) Pairwise Alignment (IGH) Pairwise Alignment via BLAST (NCBI) JDotter Pairwise Dotplot Alignment (Virology.ca) Merge two DNA sequences-Merger (EMBOSS) Multiple Alignment via ClustalW (CH.EmbNet) Similarity/Homology Analysis BLAST (NCBI) Impala Searcher to search a sequence vs Blocks-FHCRC PHYLIP - Phylogeny Analysis Structure Analysis DNA/RNA mfold analysis (IDT) Translate DNA/Open Reading Frame Analysis Translate DNA-(EMBOSS) Translate DNA – all six reading frames: Sixpack (EMBOSS) Translate DNA – (SMS) Translate DNA (ExPASy) Translate DNA (UMass) Translate DNA and ORF analysis (Colorado State) ORF Finder (NCBI) ORF Finder (SMS) ORF Analysis (UMass Best ORF (SoftBerry) Genome Analysis GATU-Genome Annotation Transfer Utility (Virology.ca) GFS –Genome-based peptide mass scanning (Virology.ca)	Amino Acid Information and Composition Amino Acid Explorer (NCBI) Amino Acid Structures and Properties (U.Berlin) Genetic Code- Standard(NIH) Amino Acid Composition - MIT Hydropathy Analysis - UCSD Isoelectric Point (pI) - ExPASy Peptide Guide - PG Peptide Statistics Tool (UMass) Statistical Analysis of Protein Sequences (EMBL) Pattern/Sequence Analysis Antigenicity Predictions (ExPASy) Eukaryotic Linear Protein Motif resource (ELM) Glycosylation sites (N-linked) (CBS) Glycosylation sites (O-linked) (CBS) Hydrophobicity Grapher (Virology.ca) MEME motif-based analysis tools Protein Motif search – FuzzPro (EMBOSS) Phosphorylation (EMBL) Post-translational Modifications Prediction (ExPASy) PSSM viewer (NCBI) Protease Cleavage (ExPASy) Sequence Searcher – motif finder (Virology.ca) TOPCONS- transmembrane topology HMMTOP-transmembrane helices and topology DAS-prediction transmembrane topology SOSUI-structure prediction transmembrane proteins PHOBIUS-transmembrane topology, signal sequence TMPred-transmembrane topology (ExPASy) Signal Sequence Prediction - CBS Signal Sequence Cleavage (UMass) Transmembrane Helices- CBS Sequence Alignment CodonAlign – nucleotide to codons (LANL) NAP nucleotide-amino acid alignment (Virology.ca) Pairwise Alignment (EMBL) Pairwise Alignment (IGH) Pairwise Alignment via BLAST (NCBI) GeneWise-alignment protein with gene Multiple Alignment via ClustalW (CH.EmbNet) Multiple Alignment via ClustalW (EMBL-EBI) Multiple Alignment via ClustalW (PIR) Multiple Alignment via COBALT (NIH) Multiple Alignment via MUSCLE (ExPASy) 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.fr – Web-based tool set (LIRMM) PhyML – generates ML trees (LANL) PhyML – Maximum Likelihood analysis (LIRMM) Structure Analysis ConSurf - Identification of Functional Regions by Surface Mapping Protein structure search with a structure (Dali) Molecular Modelling (NCBI) Protein Structure Prediction (PSIPRED) Phyre2 -Structure Prediction (ICS) Secondary Structure (Biology Workbench) - NCSA PHD Threader (Heidelberg)

Database Search Tools

Sequence Analysis Sites

· BioEdit - Multi-featured Analysis Package (Highly Recommended) Free Download

· Mega 2.1 - Multi-featured Phylogenetic Analysis Package (Free Download)

Databases

Protein and Protein Families

Genomes	Taxonomy
Ensembl genome browser SEQUENCE OF THE HUMAN GENOME (Science issue)** THE HUMAN GENOME - online resources (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/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
ExPASy – Bioinformatics Resources National Center for Biotechnology Information (NCBI)	Bioinformatics at the University of Washington Genes and Diseases (NCBI) SADR - Web based course on sequence analysis (U. Bielefeld) "Bioinformatics and Gene Sequence Analysis" PABIO536 (UW) Master's Program in Bioinformatics (Swiss Inst. Bioinformatics)

For questions and information concerning this site, please contact Dr. Timothy M. Rose, Dept. Pediatrics, University of Washington, and Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA trose@u.washington.edu. Rose Lab Web Site

Last Modified 11/3/2016 by T.Rose