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Sequence Analysis
	Other Useful Link Collections Sequence Analysis Site of Debian Wiki Remote Homology Detection PSI-BLAST PHI-BLAST Sequence Alignment and Modeling System, SAM (Richard Hughey), Documentation, Workshop HMMER (Sean Eddy) Polish Bioinformatics Site (MetaServer) The PredictProtein server: Volker Eyrich and Burkhard Rost CBS: Bioinformatics Tools Server Alignments MUSCLE (UC Berkeley) PipeAlign (Strasbourg) MView (alignment2html) Manual MultAlign: multiple alignments online; Download PipMaker and MultiPipMaker BCM Search Launcher: multiple alignments online ClustalX multiple alignments local T-COFFEE: multiple alignments online JalView: multiple alignments local & online Pileup: part of GCG ARB: rRNA alignment & phylogenetic reconstruction GeneDoc: editing tool for multiple alignments Spidey: mRNA-to-genomic BLAT: mRNA-to-genomic (under "executables" on Jim Kent's site) Sim4: mRNA-to-genomic Wise2: Genomic alignment guided by protein MRTRANS: cDNA alignment based on protein alignment Tranalign: align cDNA sequences guided by aligned protein sequences ProAlign: multiple alignments local, written in Java, runs on PC, MAC and Linux Download Alignments Trees PHYLIP, Download, Quick Guide, Manual WebPHYLIP Clustering Calculator (generates trees from distance matrices) PAUP DisplayFam: alignment and tree display on webpages (Toulouse) Link Collection for Phylogeny Programs Masking of Protein Sequences CAST SEQ (Application in GCG) Sequence Clustering BLASTCLUST PROCLUST TribeMCL GeneRAGE CD-Hit (Adam Godzik, Burnham Institute) Sequence Clustering Databases The Floral Genome Project Phytome Genome Cluster Database SYSTERS Berkeley Phylogenomics Group Genome Alignments and Visualization Generic Model Organism Database Construction Set MUMmer: fast alignment of large-scale DNA and protein sequences (TIGR) MGA: Multiple Genome Aligner (Bielefeld, Germany) LineUp: Statistical Detection of Chromosomal Homology (UCI) Vista (Visualization Tools for Alignments) Alfresco (Genome Visualization) Gene Prediction Augustus Glimmer GeneMark Genscan Computational Genomics Group (Sanger) Genotator (Berkeley) Grail (online, trained for Human, Mouse, Arabidopsis & E. coli) EST Analysis XGI - Automated sequence analysis pipeline (NCGR) stackPACK: description download DNA Editing Tools Reverse Complement of Sequence Genetic Software Links Sequence Assembly CAP3 Consed PolyPhred Phred/Phrap/Consed & UCR Manual Phred/Phrap TIGR Assembler EULER DNA/RNA Structure Chromatin Structure & Function Page RNA/DNA Folding: The Zuker Group (allows batch analysis) Vienna RNA Package Resources for non-coding RNA PatScan (Manual) RNA Family Database: Rfam INFERNAL: package to create consensus RNA secondary structure profiles ('The HMMER for RNA') RSEARCH: search tool based on both secondary structure and primary sequence COVE: old version of INFERNAL More RNA tools from S. Eddy's lab CHAOS/DIALIGN procedure; Download CHAOS plus Perl parser srnaloop (scans genomic sequence for hairpin structures), more info in publication Arabidopsis small RNA Project (Carrington Lab) Primer Design Primer3 CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primers) GeneFisher (design of degenerate primers from alignments) Batch Primer Design (Primo Pro 3.2) Link Collection Software for Promoter Motif Discovery Regulatory Sequence Analysis Tools (RSA) MotifCut (uses Maximum Density Subgraphs) Verbumculus DiAlign (aligns sequences with local similarities) LAGAN Alignment Toolkit Website FootPrinter rVista (human & mouse) BioBase ScanACE & AlignACE Consensus, ANN-Spec, Co-Bind, FoldAlign (Gary Stormo Lab) MEME & META-MEME MEME for Arabidopsis (Julian Schroeder Lab) The Gibbs Motif Sampler Homepage Gibbs Motif Sampler, Coldspring Harbor Motif Sampler Stanford BioProspector Collection at Genome Web Link Collection Page from CSL (Michael Zhang) Promoter Prediction WWW Signal Scan Neural Network Promoter Prediction Nucleotide Regulatory Region Analysis Accuracy Cister: Cis-element Cluster Finder Human Promoter Prediction: Zhang Lab Promoter & cis-Regulatory Element Databases Eukaryotic Promoter Database TESS : Transcription Element Search System Human Promoter Database Arabidopsis thaliana Promoter Binding Element Database AthaMap (genome-wide map of putative transcription factor binding sites in Arabidopsis thaliana) PlantCare PLACE AGRIS (Arabidosis Gene Regulatory Information Server) Transfac Protein Domain Prediction NetPhos: Phosphorylation Sites Protein Kinase Substrate Prediction Block Searcher NCBI Conserved Domain Database NCBI Conserved Domain Architecture Retrieval Tool Scansite Protein Targeting SoftBerry CBS Prediction Server PSORT ChloroP: Prediction of Chloroplast Transit Peptides (CBS) TargetP: Prediction of Subcellular Location of Eukaryotic Protein Sequences (CBS)
Protein Structure
	Tutorials A Guide to Structure Prediction Great Protein Structure Course Using SPDBV UCR Protein Modeling Workshop General Protein Prospector (UCSF) Structural Classification of Proteins (SCOP) Protein-protein Interaction Incyte Genomics Database of Interacting Proteins, DIP (UCLA) 2D/3D Structure Prediction HMMSTR/Rosetta Server: ab initio protein structure prediction from sequence JPRED (Barton Group) BCM Search Launcher ZPRED sss_align The PredictProtein Server UCLA/DOE Fold Server PSIPRED Protein Structure Prediction Server 3-D Structure Protein Data Bank, FTP Downloads (PDB in FASTA) Swiss-Model; Swiss-PDB Viewer (SPDBV, Deep View, Online Course); Protein Structure Course Using SPDBV Pov-Ray (creates nice images from DeepView) Short intro: save scene in SPDBV as Pov3 Scene. Open .pov file in Pov-Ray. Change in text "#version 3.x" to "#version 3.1" and set intensity at bottom of file to "rgb Intensity0.700". Hit "Run". Image will be saved automatically as .bmp file. Pov-Chem (visualization of chemicals) Rasmol (download) Chime SCOP: Structural Classification of Proteins Honig Lab Jackal: protein structure modeling package Insight II (Accelrys) Manuals Tripos, Inc. Baker Lab CASP4 Computational Genomics Group NCBI Structure Group Cn3D - NCBI's 3D structure viewer VAST - Retrieve structure alignments froom NCBI Fold Recognition* PROSPECT: threading-based protein structure prediction system PSIPRED & Threader (UCL) 3D-pssm UCLA-DOE Structure Prediction Server TOPITS (EMBL) 123D FFAS (Burnham Institute) Structure Prediction Meta Server (Polish Bioinformatics Site) Modeling Sites City of Hope List of Tools Abagyan Group Dimitrios Morikis (UCR) Teaching Modeling Biological Macromolecules(UCSD)
Transcriptional Profiling
	Microarrays General Recommendations for the Clinical Analysis of Microarray Data Link collection page The Brown Lab Software Links Experiment Design Gary Churchill's Statistical Genetics Group Minimum information about a microarray experiment - MIAME MIAME for Affy Experiments Image Analysis Array-Pro Analyzer (MediaCybernetics) ScanAlyze TIGR SpotFinder Significance Analysis SAM: Significance Analysis of Microarrays Cyber-T: Web interface to detect changes in expression data R Packages R Introduction to R (Slide Show) Learning statistical data analysis using "R" Collection of R Packages For Gene Expression Analysis BioConductor BioConductor Workshops Comparison SAM PAM Data Analysis and Data Mining Free for Academia Expression Profiler (online data mining tools from EBI) dChip (Harvard) (download) BRB ArrayTools GenePilot Cluster/TreeView (Michael Eisen) MicroArray Explorer EMBL-EBI Commercial expressionanalysis.com: Specializing in microarray analysis, bioinformatics, and expression gene profiling service. GeneSpring Avadis J-Express GeneMaths BioDiscovery Imaging Research GeneViz Lion Biosciences See also Data Mining and Network Analysis Normalization Gene Expression Data Analysis Tool and Gene Expression Data Simulator UMC Utrecht SNOMAD University of Pittsburgh Terry Speed's Microarray Data Analysis Group Page Database Tools BASE Bugzilla GeneX GeneTraffic (Iobion) NOMAD (UCSF & LBNL) MicroDB List of Databases Data Mining See Data Mining and Network Analysis Affymetrix Home Analysis Data Analysis Fundamentals (pdf) Download Microarray Suite Users Guide Version 5.0 (550 pages) Public Data Download Stanford AREX: The Arabidopsis Gene Expression Database Nottingham Arabidopsis Affy Service; Data Download List of Data Resources (Arabidopsis) Rice Expression Database Organisms Arabidopsis (CATMA) Tiling Arrays ARTADE: software for Arabidopsis tiling arrays ChipViewer (SALK) SFPs & Methods (Justin Borevitz)
Proteomics
	ExPASy Proteomics tools MS-Fit ProteinProspector X! Tandem (freeware) Mascot from MatrixScience
Metabolic Profiling
	Plant Metabolite Profiling Max Planck
Pathways
	Gene Ontology Gene Ontology Consortium Download Visualization Software for Gene Ontology and Chip Data Ontology Viewer: Onto-Express, Publication GOstat (WEHI) MAPPFinder GoMiner (NIH) Bioverse (WU) Signalling Pathways Transpath Virtual Library of Cell Biology Cancer A Subway Map of Cancer Pathways Metabolic Pathways PathMAPA (Yale University) KEGG Metabolic Pathways (ftp download) PathDB (NCGR) Biochemical Pathways PathVision WIT:Interactive metabolic pathway charts EcoCyc SoyBase IUBMB-Nicholson Minimaps GenMAPP Biocatalysis/Biodegradation Database
Databases
	General Bio-mirror (high-speed access to most "bio" databases) NCBI PubMed, FTP Downloads Batch Entrez Entrez Programming Utilities BLAST NCBI Plant Genomes Central NCBI EST Summary Ensembl EBI, FTP Downloads Pfam at Sanger, FTP Downloads (Arabidopsis: Link At# via SwissProt ID to Pfam ID) Swiss-Prot & EMBL: SWP BLAST, HTML Links, Batch download, FTP download, Swissknife (SWP Parser) Incyte Domain Databases ProDom (The Protein Domain Database): includes trees InterPro (download) PROSITE PFAM Orthologs TIGR EGO (Eukaryotic Gene Orthologs): links to KEGG and InterPro (click on sequence symbols in cluster) NCBI COGs (clusters of orthologous groups of microorganisms) Literature UCR Remote Literature Access (WebVPN) HubMed MedLine PubFetch & PubSearch (GMOD) ISI Web of Science PubMatrix MedMiner PubGene XplorMed HAPI Patents MicroPatent US Patent DialogSelect Delphion WebSPIRS Arabidopsis TIGR Annotation Page Navigate Annotation Data Download TAIR MIPS MIPS all IDs Download Garnet SALK UWBC AGRIKOLA: Systematic RNAi knockouts SNPS Cereon Full-length cDNAs: TIGR/Ceres, RIKEN, SALK AtGDB (Iowa State University) Gene Ontologies, Download, FTP-Download Arabidopsis small RNA Project (Carrington Lab) Expression Profiling Link Collection @ TAIR AtGenExpress @ TAIR Genevestigator (Gruissem Laboratory)) Nottingham Expression Data (NASC) Affymetrix Data Download: Analysis->Interactive Query->Select&All Entries->Save Affymetrix and AFGC probe sets from TAIR MPSS (Delaware Biotechnology Institute) Gene Families P450s PlantsP (SDSC) Brassica Brassica Genome Project CBC Barley Barley EST Project HarvEST Corn ZmDB Human Human Genome Central Human Genome Project Working Draft (UCSC) Full-Length Genes (Orbigen) Mouse Mouse Genome Server (EBI) Mouse Genome Resources (NCBI) Physcomitrella PEP: Physcomitrella EST Programme Populus trichocarpa JGI: Genome Database for Populus trichocarpa Rice Rice GD (spp indica) Rice Genome Research Program TIGR (spp japonica) sequence downloads: old, new, status, Pseudomolecules Syngenta (spp japonica) MIPS (spp japonica & indica) Gramene, FTP Downloads KOME (full-length cDNAs Wheat IGF
Data Mining and Network Analysis
	Freeware Pajek - Large Network Analysis Graphviz - Graph Visualization Software Rgraphviz - R Interface for GraphViz GUESS - The Graph Exploration System Cytoscape (molecular interaction networks) Osprey Commercial Applied Maths J-Express BioDiscovery GeneTraffic (Iobion) Partek Spotfire GeneSpring Rosetta Onto-Express OmniViz Molecular Mining LION Imaging Research Enodar VisWave
Free Software
	Link collections Genetic Code Table Chang Bioscience Erasmus Pedro's Data Analysis in Molecular Biology and Evolution
Tool Collections
	Molecular Population Genetics (Dick Hudson) Reverse Complementator EMBOSS: The European Molecular Biology Open Software Suite, JEMBOSS Online (MRC), UCR EMBOSS MANUAL The Sanger Centre NCBI CMS Molecular Bioology Resource The Bio ToolKit BCM Search Launcher
Genomics and Post-Genomics
	Lynx HYSEQ Illumina
Systems Biology
	The Computable Plant (Scientific Inference Systems Laboratory, UCI & Caltech) Systems Biology Workbench (Caltech) Institute for Systems Biology (Seattle) International Conferences on Systems Biology 3rd International Conference on Systems Biology (Sweden, Sweden)
Chemical Genetics
	Compound Sources Exclusive Chemistry Ltd National Cancer Institute ChemBridge Chemical Diversity Aurora Fine Chemicals See also compound source page in ChemMine Compound Binding BindingDB Compound Databases The Cambridge Structural Database NCI Database, Help for Interface, Structure Download ChemID plus (NIH) ChemBank (Harvard) ChemBridge From Hit to Lead Cheminformatics CambridgeSoft Daylight Accelrys MDL PDB Lite: Find Macromolecules SWEET (Program to construct 3D models of saccharides (DKFZ Heidelberg) Pov-Chem (visualization of chemicals) MOE (Canada) Moloc (Roche) Compound Analysis Software Chemistry Development Kit (CDK) The SDF Toolkit in Perl 5 CACTVS, Toolkit Download Open Eye Scientific Software Cambridge CCDC Products Tool Collection at SourceForge.Net JOELib (Univ. Tuebingen) Open Babel World Wide Molecular Matrix: collection of web application for calculations of molecular properties WODCA TORVS (Univ. Erlangen) Corina: 3D structure prediction of compounds (online or local) PASS: Prediction of Activity Spectra for Compounds Generate IUPAC Name from Structure (Advanced Chemistry Development) ZINC: Virtual Screening Database (UCSF) Ligand.Info: Small-Molecule Meta-Database BioScreening.com Research Labs John Weinstein Harvard Institute of Chemistry and Cell Biology (ICCB)
Cell Biology
	Protocols Protocol Online Image Informatics Open Microscopy Environment (OME, MIT) Cytoskeleton The microtubule interaction site (Brandt lab) The Kinesin Home Page Yeast Protein-Protein-Interactions (MIPS) Cell Wall CAZy Cell Wall Stanford TAIR: Cell Wall Books Ergito
Algorithms
	The Genetic Algorithms Archive
R, Latex, Perl & Python
	R R Project Site BioConductor Omegahat R Graph Gallery R & BioConductor Manual Programming in R Latex Latex Project Page Latex Packages Wiki Math Syntax Collection Formula and Equation Collection Python Python Tutorial Python Course in Bioinformatics (Catherine Letondal, Pasteur Institute) BioPython: BioPython Tutorial CherryPy EasyInstall Perl bioperl PDL: Mastering Matrices in Perl BioPerl: TIGR XML Parser Perl Course Perl Course (UCSF) Biological software developed at Pasteur Institute, e.g. seqsblast Perl by Example Promoter Extraction BLAST Parsing Perl Source (online Bioinformatics courses on Perl, Python and Java) OptiPerl EDGE Script Archive Todd Richmond (Carnegie) Xemacs CGI.pm (L. Stein) Quanta Plus (Web Page Design in Linux)
Database Software
	MySQL Tutorial dbVisualiser: graphical interface for viewing, editing and querying databases UCR MS Access Manual
Statistics
	The R Manuals Learning statistical data analysis using "R" Statistical Terms StatSoft Artificial Intelligence Depot
UNIX/LINUX
	UCR Linux Manual LinuxCommand.org Great Intro Bioinformatics and Linux course (KVL) Course on Designing Biological Databases Linux HOWTOs Linux - Red Hat UNIX Rosetta Stone Mac VersionTracker HTML HTML color codes Great HTML Editor: Quanta Symbols and Greek Letters
Courses & Meetings
	1st International Biocurator Meeting Cold Spring Harbor Genome Informatics Conference The Computational Systems Bioinformatics Conference (CSB2004, Stanford) Computational Methods in Systems Biology '04 (CMSB04) Bioinformatics Open Source Conference (BOSC) International Conference on Intelligent Systems for Molecular Biology (ISMB) International Conference on Bioinformatics and its Applications (ICBA) Philip Miller UC Davis Fralin Biotechnology Center, Virginia (Symposium, May 2002) O'Reilly Bioinformatics Technology Conference Perl Source (online Bioinformatics courses on Perl, Python and Java) Cold Spring Harbor: Lincoln Stein, Genome Informatics Computer-Aided Drug Design (UCSD)
UCR Bioinformatics Manuals
	EMBOSS GCG - SeqLab R and BioConductor Programming in R Linux Essentials Bioinfo Linux Cluster MS Access for Biologists Phred/Phrap/Consed

Thomas Girke, UC Riverside, Email: thomas.girke@ucr.edu

Center for Plant Cell Biology	Systomics Network
	Bioinformatics Core
	CEPCEB \| IIGB \| UC Riverside

Bioinformatics Links

Expression Profiling

Gene Families