Homework04 Composition

Java for Biotechnology Applications

Homework Assignment #4

1 . When data are examine from a text file, you can use the BufferedReader to learn one line each time. After a type of data� is usually read, there is not any way of going back to read this again. To overcome this you can first read each of the data into a structured target to store them, and then procedure the data afterwards. Please utilize DNA category (we allow us in the past a couple weeks, which has properties of IDENTIFICATION and seq, and the set/get methods) to build up a Java program to read in a FASTA format DNA sequence file, and parse out each sequence record into the a part of ID and sequence. The ID can be identified between " > " as well as the " |" in the header line, as well as the sequence is a concatenation of lines of the sequence part into a single line. Each GENETICS sequence record can then be stored into an array element of the DNA category. � Make use of a loop in the program to prompt you enter a chain ID, of course, if the IDENTIFICATION exists print the series. If the IDENTITY does not are present, print out a warning meaning. Exit the loop if the user gets into " quit”. Please utilize the sequence data file (seq. fasta) as the input file. Below is a sample outcome of the program: (2 points)

fastaParse. java

2 . PROSITE (http://au.expasy.org/prosite/) is a database of protein domain names, families and functional sites. Each PROSITE record is often associated with a pattern or profile to spell out the healthy proteins domain or functional internet site. Please glance at the record of PDOC00300 (http://prosite.expasy.org/PDOC00300) which is a GATA-type zinc finger domain that binds to DNA sites with the general opinion sequence (A/T)GATA(A/G). This type of " zinc finger” domains include a opinion sequence of C-x2-C-x17-C-x2-C, meaning one Cys, two virtually any amino acids, a single Cys, seventeen any proteins, one Cys, two any kind of amino acids, and one Cys. Please make use of this consensus series, and create an equivalent frequent expression design.

1) Record the regular appearance...

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