Note: You need to download and install the BioJava1.7.1 package (http://polaris.umuc.edu/~sgao/BIFS618/Homework/biojava-1.7.1_all_mod.jar), and add the required .jar files to the CLASSPATH of your sys…
Note: You need to download and install the BioJava1.7.1 package…
Note: You need to download and install the BioJava1.7.1 package (http://polaris.umuc.edu/~sgao/BIFS618/Homework/biojava-1.7.1_all_mod.jar), and add the required .jar files to the CLASSPATH of your system.
To browse all the classes in the package here: (http://nebc.nerc.ac.uk/bioinformatics/documentation/biojava/doc/biojava/index.html?org/biojava/bio/seq/io/agave/package-summary.html
1. In question #1 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 forum). 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 translate these codons into corresponding amino acid sequences. Since this type of conversion is so common in biology, BioJava has a collection of related classes to deal with DNA and protein sequences. Please review the org.java.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 readFastaDNA.java above in Q 1 to read in one or more DNA sequences from a Fasta formatted DNA sequence file (seq.fasta). (2 point)
2) The program should be able to translate three forwarding open reading frames. You can first use the transcribe() method of the GeneticCodes class to transcribe the DNA sequence into an 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 depending on which reading frame is used. You can also choose the toProtein() method in the DNATools class without adjusting the length of the sequence. (3 points