We have a group project in python programming and we have no idea how to do this.
It says its related to spelling checking program.
Text we are using: TAAGGTCA, AACAGT
And when we put it throught the terminal, it must show like the last picture.
Project The purpose of this project is to write a program to compute the optimal sequence alignment of two DNA strings. This program will introduce you to the emerging field of computational biology in which computers are used to do research on biological systems. Further, you will be introduced to a powerful algorithmic design paradigm known as dynamic programming Biology Review A genetic sequence is a string formed from a four-letter alphabet Adenine (A) Thymine (T), Guanine (G), Cytosine (C) of biological macromolecules referred to together as the DNA bases. A gene is a genetic sequence that contains the information needed to construct a protein. All your genes taken together are referred to as the human genome, a blueprint for the parts needed to construct the proteins that form your cells. Each new cell produced by your body receives a copy of the genome. This copying process, as well as natural wear and tear, introduces a small number of changes into the sequences of many genes. Among the most common changes are the substitution of one base for another and the deletion of a substring of bases; such changes are generally referred to as point mutations. Because of these point mutations, the same gene sequenced from closely related organisms will have slight differences. The Problem Through your research you have found the following sequence of a gene in a previously unstudied organism A A CAG T TAC C What is the function of the protein that this gene encodes? You could begin a series of uninformed experiments in the lab to determine what role this gene plays. However, there is a good chance that it is a variant of a known gene in a previously studied organism. Since biologists and computer scientists have laboriously determined (and published) the genetic sequence of many organisms (including humans), you would like to leverage this information to your advantage. We'll compare the above genetic sequence with one which has already been sequenced and whose function is well understood TAA G G T C A If the two genetic sequences are similar enough, we might expect them to have similar functions We would like a way to quantify similar enough." Edit Distance In this assignment we will measure the similarity of two genetic sequences by their edit distance, a concept first introduced in the context of coding theory, but which is now widely used in spell checking, speech recognition, plagiarism detection, file revision, and computational linguistics. We align the two sequences, but we are permitted to insert gaps in either sequence (e.g., to make them have the same length). We pay a penalty for each gap that we insert and for each pair of characters that mismatch in the final alignment. Intuitively, these penalties model the relative likeliness of point mutations arising from deletion/insertion and substitution. We Page 1
