Midterm Solutions Fall 2016

PwnHero BME501/CPS501 Bioinformatics Midterm, Oct. 24, 2016 Family Name:_____________ First Name: _____________ Student Number: ____________ Answer all questions in the question booklet, right below the question. No aids of any kind, including no calculators. 1. Database (20 points) (a) Write a query for the NCBI Nucleotide database which has a good chance of resulting in a single record which is the reference sequence DNA for the myoglobin gene in humans. (3 points) myoglobin[title] AND homo sapiens [title] AND refseqgene[keyword] (b) In the record returned for query (a), I see in the first three lines “NG_007075”. What is the name of that code and what is its purpose? (3 points) That is an accession number which can be used to locate this gene in the database. (c) On the first line of record (a) I see “23591 bp DNA linear”. What does that mean? (3 points) This record is for 23591 base pairs of DNA. (d) Under Features of record (a) I see “gene 5001 .. 21591”. What does that mean? (3 points) The part of the DNA shown in this record from position 5001 to 21591 is the actual gene. (e) Under Features of record (a) I see “mRNA join(5001..5164, 11090..11192, 17249..17471, 20912..21591)”. What does that mean? What are those subsequences? (5 points) The mRNA is made up of the four subsequences shown, and those are the exons. (f) How long is the coding sequence, or can you not say given this much information? (3 points) You cannot say, since the first and last exons probably contain untranslated regions. 2. Data mining (25 points) Consider the following table, which is modified from “Data Mining”, by Tan, Steinbach and Kumar. In the following questions, ignore the Name column. Assume that we want a model which predicts “Class” as mammal or non-mammal. 1 PwnHero.com