Dna sequences, Computer Engineering

The dataset provided in this assignment contains a collection of real DNA sequences. The number of true binding sites is quite limited and that makes the problem challenging. In machine learning community, this is termed as imbalanced datasets. Some techniques dealing with imbalanced data classification, such as sampling or filtering, can be applied for the biological data. It is a good idea to find some relevant publications to see in which way you can build effective classifiers for motif recognition.

The whole dataset should be partitioned into a training dataset used to build the learner models, and a testing dataset used to evaluate generalization capability of the classification systems. System performance will be evaluated by looking at the recall, precision, F-measure and recognition rate for both the training dataset and the test dataset.

It is very important to notice that unlike traditional way for evaluating classifier's performance, here a kmer is classified as a motif instance if its location has at least 50% overlap with a true binding site in the DNA sequences. For example, consider two true binding sites ACACGGGA and ACACGGGA in the following DNA sequence.

ccttacacaaACACGGGAgaattaatACACGGGAtcagatcaataaa (1)

Suppose that the 8mers acaaACAC and ACGGGAtc are classified as binding sites by a learner model. Then, we will count them as correct prediction because they have 50% and 75% overlaps with the true binding sites in sequence (1), respectively. Conversely, if classifiers classify them as non-binding sites, then we will count them as incorrect prediction because they have at least 50% overlaps with the true binding sites. Take another 8mer, GAgaatta, in (1). If it is classified by a learner model as a binding site, then it will be counted as a misclassified one because it has only 25% overlap with the true binding site ACACGGGA

Posted Date: 3/29/2013 5:36:08 AM | Location : United States







Related Discussions:- Dna sequences, Assignment Help, Ask Question on Dna sequences, Get Answer, Expert's Help, Dna sequences Discussions

Write discussion on Dna sequences
Your posts are moderated
Related Questions

At a shop of marbles, packs of marbles are prepared. Packets are named A, B, C, D, E …….. All packets are kept in a VERTICAL SHELF in random order. Any numbers of packets with thes

Give the format of ICMP header and explain meaning of each field. The format of ICMP header is given below: Internetwork Control Message Protocol (ICMP) ICMP H

Q. Writing down your own Interrupt Service Routines? Here are a few rules which should be kept in mind while writing down your own Interrupt Service Routines: 1.  Use Int 21

In computing, virtual memory is a memory management method developed for multitasking kernels. This technique virtualizes computer architecture's various forms of computer data sto

Parallelism Conditions As discussed earlier, parallel computing needs that the segments to be implemented in parallel must be free of each other. Thus, before implementing para

Q. What is Memory Address Register? Memory Address Register (MAR): It specifies address of memory location from that data or instruction is to be accessed (read operation) or t

Binary Search Now that the basic framework is working, it is time to begin implementing a few alternative search functions. Each of these search algorithms have strengths and

Write a program to find the area under the curve y = f(x) between x = a and x = b, integrate y = f(x) between the limits of a and b. The area under a curve between two points can b

Uniform Memory Access Model (UMA) In this model, the main memory is uniformly shared by all processors in multiprocessor systems and each processor has equal access time to sha