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MBoMS Genomics of Model Microbes Lab 1: Genome databases Quic kTime™ and a TIFF (Unc ompres sed) dec ompres sor are needed to see this pic ture. QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Genomics of Model Microbes Instructor: Peg Riley [email protected] Section grade 20% lab notebook 20% homework 60% independent project Model Microbes and the Microbial Species Concept • We are going to employ model microbes and their genomes to begin to address the microbial species concept – What you learned from my presentation is that such a study requires us to be able to handle very large databases of sequences and to compare them between individuals within a species and between multiple species • Our goal is to provide robust answer to the question “Do microbes adhere to a Molecular Databases • The first step in our study is to learn how to find the existing molecular databases – In our case, microbial genomes • Let’s start with an introduction to molecular databases – One of the most challenging tasks faced by molecular biologists comes after the data has been collected – Data recording, storage, analysis and interpretation require the use of sophisticated software and hardware – For example: • GenBank holds over 130 billion bases • Genome Project holds over 1,360 complete/incomplete genomes Biological databases • In this portion of the course, we will learn how to negotiate your way through massive biological datasets with ease QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. www.bio-pro.de/imperia/ md/images/artikelgebun... What is a biological database? • A large, organized body of persistent data – usually associated with computerized software designed to update, query, and retrieve components of the data stored within the system Biological database – A simple database might be a single file containing many records, each of which includes the same set of information • For example, a record associated with a nucleotide sequence database typically contains information such as contact name, the input sequence with a description of the type of molecule, the scientific name of the source organism from which it was isolated, and often, literature citations associated with the sequence GenBank Accession • • • • • • • • • • • • LOCUS NM_001042765 1406 bp mRNA linear PRI 11-FEB-2007 DEFINITION Macaca mulatta alcohol dehydrogenase 1A (class I), ACCESSION NM_001042765 XM_001106395 VERSION NM_001042765.1 GI:112363121 KEYWORDS . SOURCE Macaca mulatta (rhesus monkey) ORGANISM Macaca mulatta Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Cercopithecidae; Cercopithecinae; Macaca. REFERENCE 1 (bases 1 to 1406) AUTHORS Cheung,B., Holmes,R.S., Easteal,S. and Beacham,I.R. TITLE Evolution of class I alcohol dehydrogenase genes in catarrhineprimates: gene conversion, substitution rates, and gene regulation JOURNAL Mol. Biol. Evol. 16 (1), 23-36 (1999) PUBMED 10331249 • FEATURES source • gene • CDS Location/Qualifiers 1..1406 /organism="Macaca mulatta" /mol_type="mRNA" /db_xref="taxon:9544" /chromosome="5" /map="5" 1..1406 /gene="ADH1A" /note="alcohol dehydrogenase 1A (class I),polypeptide" /db_xref="GeneID:707682" 24..1151 /gene="ADH1A" /EC_number="1.1.1.1" /note="alchohol dehydrogenase 1A" /codon_start=1 /product="class I alcohol dehydrogenase, alpha subunit" /protein_id="NP_001036230.1" /db_xref="GI:112363122" /db_xref="GeneID:707682" /translation="MSTAGKVIKCKAAVLWEVMKPFSIEDVEVAPPKAYEVRIKMVTV GICGTDDHVVSGTMVTPLPVILGHEAAGIVESVGEGVTTVEPGDKVIPLALPQCGKCR ICKTPERNYCLKNDVSNPRGTLQDGTSRFTCRGKPIHHFLGVSTFSQYTVVDENAVAK IDAASPMEKVCLIGCGFSTGYGSAVKVAKVTPGSTCAVFGLGGVGLSAVMGCKAAGAA RIIAVDINKDKFAKAKELGATECINPQDYKKPIQEVLKEMTDGGVDFSFEVIGRLDTM MASLLCCHEACGTSVIVGVPPDSQNLSINPMLLLTGRTWKGAVYGGFKSKEDIPKLVA DFMAKKFSLDALITHVLPFEKINEGFDLLRSGKSIRTILTF" polyA_site 1406 /gene="ADH1A" • ORIGIN tgcaaagcag gcacctccta gatgaccacg gcagccggca gtcatcccac aactactgct aggttcacct tacacggtgg gtctgcctta gtcaccccag atgggctgta tttgcaaagg cccatccagg atcggtcggc agcgtcatcg ctgactggac ccaaaacttg gttttacctt cgtaccatcc ctcctctacc agatgtattc ttatttttca ctggggaatt 1 61 121 181 241 301 361 421 481 541 601 661 721 781 841 901 961 1021 1081 1141 1201 1261 1321 1381 tgcagagaag ctgtgctatg aggcttatga tggttagtgg ttgtggagag tcgctcttcc tgaaaaacga gcagggggaa tggatgagaa ttggctgtgg gctctacctg aagcagctgg ccaaagagtt aggtgctaaa ttgataccat taggggtacc gcacctggaa tggctgattt ttgaaaaaat tgaccttttg ctacatgatc aataaattac agcaaaaatt gagccaataa accagaaacc ggaggtaatg agttcgcatt taccatggtg tgttggagaa tcagtgtgga tgtgagcaat gcccatccac tgcagtagcc attttcaact tgctgtgttt agcagccaga gggtgccact ggaaatgact gatggcttcc tcctgattcc gggggctgtt tatggctaag aaatgaaggc aaacactaga tggagcaaca acatgggggc taaaattcaa actgttcttc aacatgagca aaaccctttt aagatggtga accccacttc ggggtgacta aaatgcagaa cctcggggga cacttcctcg aaaattgacg ggttatgggt ggcctgggag atcattgcgg gaatgcatca gatggaggtg ctgttatgtt cagaacctct tatggtggct aagttttcac tttgacctgc gatgccttcc gctgggaaat tttccaaaga gtgagaatta tcaacc// cagcaggaaa ccattgagga ctgtaggaat ctgtgatttt cagtcgaacc tttgtaaaac ccctgcagga gtgtcagcac cagcctcacc ctgcagtcaa gggtcggcct tggacatcaa accctcaaga tggatttttc gtcatgaggc caataaaccc ttaagagtaa tggatgcttt ttcgctctgg cttgtacgca atcataattc aatggcaaat aataaagtgt agtaatcaaa tgtggaggtt ctgtggcaca aggccatgag aggtgataaa cccggaaagg tggcaccagc cttctcccaa catggagaaa agttgccaag atctgctgtt caaggacaaa ctacaagaaa gtttgaagtc atgtggcaca tatgctgcta agaagatatc aataacccat gaaaagtatc gtcttcaggc tgctcttcag tgatgggaaa tgaacatcag Biological database –For researchers to benefit from the data stored in a database, two additional requirements must be met: • easy access to the information • a method for extracting only that information needed to answer a specific biological question There is an enormous diversity of molecular databases DNA sequences QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Genome sequences QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. • www.sanger.ac.uk/.../ 050304_bfragilis-300.jpg Protein sequences QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. • www.accelrys.com/.../ images/blast_sm.jpg RFLP data QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. • biologi.uio.no/.../ Images/RFLP.FIG3.gif SNPs Single nucleotide polymorphism 1: rs33873737 [Mus musculus] Links GCTTTCCACAGAAGCTTGATGACTT[A/G]AATTCTATCCTTAGAACCCACTTAA 2: rs33871597 [Mus musculus] Links TGTAGGCTTTCTGTTGTTTTTGTTG[C/T]TATTGAAGACCAGCCTTAGTCCTTA 3: rs33871077 [Mus musculus] Links CATTTCAAATGTTATCCTCTTTCCA[C/T]GACCCCCCCAAACACCCTATCCCAT 4: rs31664163 [Mus musculus] Links TGTAATTGGTAAACTTGTAATTTTT[A/T]AAGGAAGATTTGTATATTTTCCCCT Molecular structure QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. • www.cs.dartmouth.edu/.../ proj/insulinLabels.gif Microarrays QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. • www.bio-aurum.com Gene networks QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. • www.ehponline.org/txg/ members/2004/6758/fig3.gif Exercise 1 • Introduction to NCBI Open NCBI http://www.ncbi.nlm.nih.gov/ – Go to the NCBI introduction http://www.ncbi.nlm.nih.gov/About/index.html – Glance at the 7 sections and provide answers to the tasks and questions listed below 1. NCBI at a glance - what is the mission of NCBI? 2. A science primer - briefly describe each of the science primers 3. Databases and tools - create a list of databases and related resources described 4. Human genome resources - what sorts of things can you learn at the HGR site 5. Model organisms guide - how many model organisms are there? 6. Outreach and education - what tutorials are offered? 7. News - what is the latest news at NCBI? Exercise 2 • Use Connexions web-based learning tools to explore NCBI and other data repositories – Bio 533 Bioinformatics by Susan Cates http://cnx.org/content/col10152/latest/ • Go to the Database lab and complete each of the 4 sections 1. 2. 3. 4. NCBI orientation Entrez, problems 1-12 Protein data bank, problems 1-12 Tour of bioinformatics sites, problems 1-2 Exercise 3 • Use NCBI to learn about microbial genome databases – Click on “All databases” – Click on “Genome” • Become familiar with the genome resources offered by NCBI • How many complete genomes are now available • Pick one genome you are surprised to see and explain why Exercise 4 – Click on “New Microbial Genome Resources” • Become familiar with the contents • How many complete microbial genomes are there? • Do you see a bias in what genomes are available? – What is gMap? • What does this tool provide? • When might it be useful? • Use Escherichia to view the output of gMap and summarize your findings » How many genomes are compared? » What does hit coverage limit mean? Exercise 4 cont. – What is genome ProtMap? • What does this tool provide? • When might this feature be useful? – How many bacterial protein clusters are known? • Use COG0539 in ProtMap and summarize what you find Exercise 5 • Independent Projects • You will now be assigned a pair of microbial species – Research the basic biology of both species – Provide a one page summary of what you learn • Find one genome for each species – Provide a summary description of these genome • Include size, number of proteins encoded, base composition, etc. • Determine if there are multiple genomes for each species – Provide a one page description of how many genomes are available, how they differ and how they are similar • Hint, you may have to do some genome comparisons using the tools you just learned about! Model Microbial Species Bacterial Species Acinetobacter baumannii Bacillus anthracis Bacillus cereus Buchnera aphidicola Burkholderia cenocepacia Burkholderia mallei Burkholderia pseudomallei Campylobacter jejuni Chlamydia trachomatis Chlamydophila pneumoniae Clostridium botulinum Clostridium perfringens Corynebacterium glutamicum Ehrlichia ruminantium Escherichia coli Francisella tularensis Haemophilus influenzae Helicobacter pylori Legionella pneumophila Methanococcus maripaludis Mycobacterium tuberculosis Neisseria meningitidis Prochlorococcus marinus Pseudomonas aeruginosa Pseudomonas putida Pseudomonas syringae Rhodobacter sphaeroides Rhodopseudomonas palustris Salmonella enterica Shewanella baltica Staphylococcus aureus Streptococcus agalactiae Streptococcus pneumoniae Streptococcus pyogenes Streptococcus thermophilus Xanthomonas campestris Xylella fastidiosa Yersinia pestis Yersinia pseudotuberculosis Number Complete Genomes 3 3 4 4 3 4 4 5 3 4 6 3 3 3 13 7 4 3 4 4 4 4 12 3 4 3 3 5 6 3 14 3 4 12 3 3 3 7 3 Lab Notebook • You will create a lab notebook to keep track of your laboratory exercises and assignment • For each exercise you should start a new page and put the exercise “title”, your name and the date – Include enough information about the exercise so that someone who picks up your notebook could repeat your investigations • In other words, just labeling the parts 1, 2, etc. won’t do it – Explain what you are doing and how you do it • Provide detailed information about the steps you take – Summarize each exercise with a paragraph about the most important things that you learned • We will examine your notebook at each class