Download BTEC 3301 Spring 2009 HW02 Solution: Sequence & Info Retrieval and Gene Finding and more Assignments Biotechnology in PDF only on Docsity! BTEC 3301, Spring 2009 HOMEWORK 02 SOLUTION Sequence & Information Retrieval & Prokaryotic Gene Finding This assignment will assess your understanding of searching the biomolecular databases to retrieve sequence information, and for finding genes in the prokaryotic genome. What to submit: Hard Copy of your answers, include your Name & student ID IMP Note: Please include the DATE and TIME of when you performed the searches to get your answers. Points will be deducted if you fail to do so. 1. Using NCBI ENTREZ, select the GENOME database, and find out the general molecular function of aroE in the species Agrobacterium tumefaciens str. C58. What is the function? (10 points) AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate 2. Using NCBI ENTREZ, find out on which chromosome in Drosphila melanogaster do the genes amnesiac (amn) and dunce (dnc) lie? In which, biological processes are they involved? (10 points) Chromosome X amn is required in initiation and maintenance of sleep. Age-related memory impairment in flies results from a specific decrease in amn-dependent middle-term memory. Dunce is involved in short-term memory formation. 3. Using NCBI ENTREZ, find the list of extinct organisms archived. Go to extinct Insects and select ‘Libanorhinus succinus (a beetle from Lebanese amber 120-1135 Mya). (8 points) What is the ancestry of this organism ? Lineage( full ) cellular organisms; Eukaryota; Fungi/Metazoa group; Metazoa; Eumetazoa; Bilateria; Coelomata; Protostomia; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Curculionoidea; Nemonychidae; Libanorhinus How many nucleotide sequences are listed ? 1 What is the name of the gene on the sequence? gene="18S rRNA” 4. Using SRS answer the following. Describe search field terms and operations use for each search. (12 points) a. How many Bacillus subtilis sequences does SwissProt contain? 3593 b. How many of these are not hypothetical? 3563 c. How many from (a) are signal peptidases from B. subtilis in SwissProt. 9 d. How many from (c) are B. subtilis signal peptidase I sequences. 7 Solution Search for Bacillus subtilis, in the organisms field - not the species field. Hypothetical proteins in SwissProt (usually) have the keyword hypothetical. Combine searches with BUTNOT. "Signal peptidase" can be found in the description field of the signal peptides 5. Prokaryotic Gene Finding: The objective of this exercise is to develop a critical attitude towards annotations and gene finders. Even though gene finding in prokaryotes is very simple compared to eukaryotic gene finding there are multiple things that can go wrong. Use the sequence from a E. Coli plasmid available on the class web page (seqHW02.fasta). Generally you expect genes in E. coli to be in the range 100 - 500 amino acids. I. Run the NCBI ORF Finder (20 points) (a) How many ORFs can you find that > 300 nts in length? (b) What are their start coordinates? Shown above Do they all start with Methionine (Met, M)? Yes, except for the one at Frame -3, 1-1267. (c) Can you identify any long ORFs? Look for length, and start and stop codons, without any stop codons inbetween. (d) How do you tell which of these ORFs - are real protein coding genes?
