Java Programming

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BIFS618-9040: Java for Biotechnology Applications Spring 2016 Homework Assignment #5 Due Date: 04/17/2016 8 points toward your final grade Please read the instructions below before starting the assignment: Post the assignment on your LEO's Assignments homework folder: In general, you need to post the finished homework assignment on the LEO's Assignment folder. This is necessary because a grade can only be given against a posted assignments in LEO. What to post in LEO: Submit this word document file (such as: Homework01.doc) to the assignment folder with all the questions answered if the questions are not Java programs. For those questions need to write Java programs or generate results in an output file, please write down the file name(s) in each question area and then submit the .java source files as attachments. How to name your Java program file: For the questions need to write Java programs, please name your file following this naming convention: hwkx_y.java, where “x” is the number of the homework assignment and “y” is the question number, such as hwk3_4.java indicates a program for homework3, question #4. For the programs that need additional class files, please name the class file accordingly. Your programs should be executable and without compilation and runtime errors. Programming with Style: Programming style will be evaluated towards the grade. Your Java programs should be easy to read and well commented. You need to have these lines in the beginning of each program as comments: Class Name: Homework assignment#, question# File name: Program author name: IMPORTANT: Please finish your assignment on time. Late submission will result in point deductions as specified in the Syllabus. Note: You need to download and install the BioJava1.7.1 package (http://biojava.org/wiki/BioJava:GetStarted), and add the required .jar files to the CLASSPATH of your system. To browse all the classes in the package (http://www.biojava.org/docs/api171/) 1. In question #2 of homework04, you are asked to read a Fasta format DNA sequence file with 6 records (seq.fasta). BioJava has made this type of operation much simpler (see the java program: readFastaDNA.java, in the In-Class exercises main topic under week10-11 conference). With little modification to that program, please develop a Java program to read a GenBank format DNA sequence file (GenBank_seq.gb), and extract the GenBank accession number, the length of the sequence, and the description of the sequence (all printed on the first line) and sequence itself to be printed as a separate line.( 3 points) 2. In homework03, you are asked to write two methods for a DNA class, codon() and codon2aa() to parse a piece of DNA sequence into codons of three reading frames and then translate these codons into corresponding amino acid sequences. Since this type of conversions is so common in Biology, BioJava has a collection of related classes to deal with DNA and protein sequences. Please review the org.biojava.bio.symbol, and org.biojava.bio.seq packages (mainly the DNATools, RNATools, and the GeneticCodes classes) to develop a Java program to translate a DNA sequence into its corresponding protein sequence. 1) The program should incorporate the functionality of getting a DNA sequence from NCBI with a provided GenBank Accession number (see the Java program: fetchGenBank.java, in the In-Class exercises main topic under week10-11 conference). (2 point) 2) The program should be able to translate three forwarding open reading frames. First use the transcribe() method of the GeneticCodes class to transcribe the DNA sequence into a RNA sequence, and then use the translate() method to translate it into a protein sequence. Please note that the translate method only takes a sequence with a length divisible by 3, so you need to adjust the length of the sequence depends on which reading frame is used. (3 points)

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Mike_kassidy
School: Carnegie Mellon University

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Anonymous
Awesome! Exactly what I wanted.

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