MICROBES ONLINE Virtual Institute for Microbial Stress and Survival Site Guide & Tutorial MICROBESONLINE Site Guide & Tutorial 2008 Virtual Institute for Microbial Stress and Survival, http://vimss.lbl.gov • http://www.microbesonline.org Ernest Orlando Lawrence Berkeley National Laboratory 1 Cyclotron Road • Berkeley, CA 94720 Table of Contents SITE OVERVIEW ............................................................................................................... 2 SYSTEM REQUIREMENTS .......................................................................................................... 2 SITE PRIVACY POLICY ............................................................................................................ 3 DATA RELIABILITY DISCLAIMER ................................................................................................ 3 DNA Sequences .................................................................................................... 3 Protein-coding Gene Predictions........................................................................ 4 Non-coding RNA Gene Predictions .................................................................... 4 Protein Homology.................................................................................................. 4 Gene Names & Descriptions................................................................................ 5 EC Assignments & Metabolic Maps .................................................................... 5 Orthologs................................................................................................................ 6 Operon Predictions ............................................................................................... 6 Regulon Predictions .............................................................................................. 6 Gene Expression Data (Microarrays) .................................................................. 6 HOME PAGE.................................................................................................................... 7 TOP NAVIGATION .................................................................................................................. 7 Login ....................................................................................................................... 8 Register................................................................................................................... 9 My Gene Carts ...................................................................................................... 9 Sequence Search ................................................................................................. 9 Advanced Search................................................................................................. 9 Contact Us ............................................................................................................. 9 GENOME SELECTOR .............................................................................................................. 9 Configuring Your Own Set of Favorite Genomes............................................ 10 Finding Genes...................................................................................................... 12 Genome Actions: Info ........................................................................................ 14 Genome Actions: GO......................................................................................... 14 Genome Actions: Pathways .............................................................................. 14 QUICK SEQUENCE SEARCH ..................................................................................................14 ABOUT MICROBES ONLINE ...................................................................................................15 MICROBES ONLINE HIGHLIGHTS ............................................................................................15 SEQUENCE SEARCH...................................................................................................... 15 PROTEIN SEQUENCE SEARCH RESULTS ...................................................................................16 Near-Exact Matches........................................................................................... 17 Domain Hits .......................................................................................................... 17 Distant Homologs ................................................................................................ 18 NUCLEOTIDE SEQUENCE SEARCH RESULTS .............................................................................19 BLAST SEQUENCE SEARCH ..................................................................................................19 Filter Low Complexity.......................................................................................... 21 Mask For Lookup Table Only .............................................................................. 22 Expect................................................................................................................... 22 Matrix .................................................................................................................... 22 Perform Ungapped Alignment.......................................................................... 22 Genetic Codes.................................................................................................... 22 Frame Shift Penalty.............................................................................................. 22 BLAST Sequence Search Results ........................................................................ 22 ADVANCED SEARCH.................................................................................................... 24 GENOME INFORMATION ............................................................................................. 25 SUMMARY VIEW ..................................................................................................................26 SINGLE -GENOME DETAIL VIEW ............................................................................................27 GENE LIST VIEW ..................................................................................................................28 GO BROWSER................................................................................................................ 29 ONTOLOGY BROWSER VIEW ................................................................................................30 GENE LIST VIEW ..................................................................................................................31 TUTORIAL : FINDING GENES ASSOCIATED WITH A GO TERM ....................................................32 PATHWAY BROWSER..................................................................................................... 32 MAP VIEW ..........................................................................................................................33 GENE LIST VIEW .................................................................................................................34 F TUTORIAL : IDENTIFYING METABOLIC DIFFERENCES BETWEEN TWO GENOMES ...........................34 TUTORIAL CASE STUDY : FREE -LIVING VS . ENDOSYMBIONT .......................................................35 SPECIES TREE ................................................................................................................. 35 LOCUS INFORMATION.................................................................................................. 38 COMMON NAVIGATION .....................................................................................................38 GENE INFO .........................................................................................................................39 OPERON & REGULON .........................................................................................................41 Predicted/Confirmed Operons ......................................................................... 41 Predicted Regulons............................................................................................. 42 Enriched GO Terms ............................................................................................. 42 DOMAINS & FAMILIES ..........................................................................................................43 Locus HMM Alignment Viewer........................................................................... 44 Locus PDB Alignment Viewer............................................................................. 45 HOMOLOGS .......................................................................................................................45 SEQUENCES ........................................................................................................................48 ADD ANNOTATION ..............................................................................................................48 TREE BROWSER .............................................................................................................. 49 GENE TREE OPTIONS ...........................................................................................................49 Tree Options......................................................................................................... 49 Coverage............................................................................................................