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Tools for BioInformatics Eileen Kraemer Computer Science Dept. The University of Georgia Types of Tools Lab samples Production Sequencing Software Sequence data Databases, Database Search Tools Production Sequencing Software used throughout the sequencing procedure from preparation of the DNA through to the finishing of clones. Example: Sanger Centre, Shotgun Sequencing of typical human clone Data collection Transfer to UNIX Gel image processing Sequence pre-processing DNA Fragment Assembly Editing Finishing Services Quality Control and Assesment Databases Swiss-Prot EMBL Entrez GDB GenBank GSDB PDB & more -- see links at: http://www.public.iastate.edu/~pedro/rt_1.html Species-specific Databases See: http://genetics.about.com for both: Non-human and human genome projects Examples: PomBase is a compilation of data relating to the organism Schizosaccharomyces pombe Wormpep predicted proteins from the C. elegans genome sequencing project. Annotation Tools Annotation of sequences with info such as homologies to known genes, possible gene locations, gene signals such as promoters, etc. Example: Genotator (Nomi Harris) -- developing a workbench for automatic sequence annotation and annotation viewing and editing. The goal is to run a series of sequence analysis tools and display the results in such a way that the various predictions can be compared, and researcher makes decision of what to include. Database Software ACEDB is an acronym for "A Caenorhabditis elegans DataBase". It can refer to a database and data concerning the nematode C. elegans, or to the database software alone. Other groups may adapt existing, or create own. For example, David Hall’s workflow project at UGA for Neurospora Types of Tools Sequence Structure Function Gene Prediction Caution: accuracy <= ~ 70% Good review: Snyder and Stormo, (chapter 11 of the book Nucleic Acid and Protein Sequence Analysis: A Practical Approach, second edition, 1994. ) Gene Prediction GRAIL(Xgrail, JavaGrail, etc.) Geneid Netgene GenMark Fexon, Hexon GENSCAN xpound Genefinder (University of Washington) GRAIL Predicts coding regions Uses a neural network which combines a series of coding prediction algorithms. recognizes coding potential within a fixed size (100 base) window; evaluates coding potential without looking for additional features later versions incorporate additional info human and other species GeneMark Based on inhomogeneous Markov models predicts coding and non-coding regions based on statistical patterns in dinucleotide frequences … more next week from Mark B. Sequence Alignment Pairwise alignments Multiple sequence alignments Pairwise Alignments SIM (Protein only) - k best non-intersecting alignments (EXPASY) ALIGN - optimal global alignment with no short-cuts (EERIE) LALIGN - calculates the N-best local alignments (EERIE) LFASTA - local similarity searches showing local alignments (EERIE) BLAST 2 - local alignment using BLAST (NCBI) LAP2 - local DNA to protein alignment with LAP2 (MTU) Multiple Sequence Alignments ClustalW 1.7 (DNA/Protein) - Global progressive (BCM) CAP Sequence Assembly (DNA) - Contig Assembly MAP (DNA/Protein) - Global progressive in linear space PIMA 1.4 (Protein only) - Pattern-Induced (local) Multiple Alignment (BCM) MSA 2.1 (Protein only) - Near-optimal sum-of-pairs global (WashU) BLOCK MAKER (Protein only) - Finds conserved blocks in seq sets (FHCRC)ClustalW 1.7 (DNA/Protein) Global progressive (BCM) MEME 2.2 (DNA/Protein) - Multiple EM for Motif Elicitation (SDSC) Similarity Searching BLAST -- (BLASTP, TBLASTN, etc.) a nucleotide or protein sequence sent to the BLAST server is compared against and a summary of matches is returned to the user. allows all combinations of DNA or protein query sequences with searches against DNA or protein databases: BLAST variations blastp compares an amino acid query sequence against a protein sequence database. blastn compares a nucleotide query sequence against a nucleotide sequence database. blastx compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database. tblastn compares a protein query sequence against a nucleotide sequence database dynamically translated in all six reading frames (both strands). tblastx compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database. Types of Tools Sequence Structure Function Protein Structure Prediction Ab initio -- based on energy minimization fold recognition -- sequence -> secondary structure, then align secondary structures with corresponding secondary structures in related proteins, etc. statistical -- based on “hidden patterns”; similar patterns -> similar structure Protein Secondary Structure Prediction Coils - prediction of coiled coil regions nnPredict - uses a 2 layer neural network PSSP / SSP - segment-oriented prediction PSSP / NNSSP - nearest-neighbor prediction SAPS - statistical analysis of protein sequences Paircoil - coiled coil regions of pairwise residue correlations Protein Hydrophilicity /Hydrophobicity SOPM - self optimized prediction method Types of Tools Sequence Structure Function Protein Function Prediction Pfam groups of similar function proteins aligned and HMMs generated for each “cluster” HMM generated for unknown function protein and compared to HMMs of known proteins for predicted function classification Pfam components PROTEIN HMM SEARCH - Analyze a protein query sequence to find Pfam domain matches. DNA HMM SEARCH - Analyze a DNA query sequence to find Pfam domain matches. (Uses the GeneWise server at the Sanger Centre.) BROWSE PFAM - View Pfam annotation and alignments. TEXT SEARCH - Query Pfam by keywords. BROWSE SWISSPFAM - View the domain organization of any SWISSPROT/TrEMBL sequence according to Pfam. Types of Tools Sequence Sequence Sequence Sequence Across organisms … Phylogeny Reconstruction Phylogeny Reconstruction Construct evolutionary trees based on divergences that occur in related sequences parsimony, minimum distance, etc. parsimony -- construct tree so that number of mutation events is minimized PHYLIP, PAUP, others, some interactive Visualization Tools Database viewers Sequence viewers Molecular viewers Physical Mapping Software used to physically locate genetic markers. FPC Software for FingerPrinting Contigs. Image 3.x Software for processing fingerprint gel images. RHServer This web interface positions one or more markers on the 1998 International Gene Map (GB4). SAM System for Assembling Markers. SAM takes as input a set of clones and their associated markers, and outputs a partially ordered marker map. Z-RHMAPPER Extensions to the RHMAPPER (Whitehead) Radiation Hybrid Mapping Package. Good Resources Pedro’s BioMolecular Research http://www.public.iastate.edu/~pedro/rt_1.html BCM pages www.hgsc.bcm.tmc.edu/SearchLauncher/index.html Sanger Center www.sanger.ac.uk/Software/Sequencing/overview.shtml Mining Co. Web Site genetics/miningco.com & many others