bioinformatics.md

Introduction

Inexact or appropriate matching means some errors will be there

Alignment generally means lining up characters of strings, allowing mismatches as well as matches, and allowing characters of one string to be placed opposite spaces made in opposing string

It is central in computational molecular biology because of active mutational process

Duplication and modification is the central part of protein evolution

In DNA/RNA/Amino Acid sequences, high sequences, high sequence similarity implies significant functional or structural similarity

Edit distance between two strings

Difference between two strings

It focuses on transforming (or editing) one string into the other by a series of edit operations on individual characters

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The permitted edit operations are insertion, deletion, and replacement

For match operation no operation is necessary

Edit Transcript: A string over the alphabet I, D, R, M that describes a transformation of one string to another is called an edit transcript, or transcript for short, of the two strings

Edit Distance: The minimum number of edit operations--insertions, deletions, and substitutions--needed to transform the first string into the second. Also know as Levenshtein distance

Optimal Transcript

Optimal transcript is an edit transcript that uses minimal number of edit operations

There may be more than one optimal transcript for two strings

String Alignment

A global alignment of two strings S1 and S2 is obtained by first inserting chosen spaces, either into or at the ends of S1 and S2, and then placing two resulting strings one above the other so that every character or space in either string is opposite a unique character or a unique space in the other string

Alignment vs Edit transcript

Mathematical viewpoint these are equivalent ways to describe relationship between two strings

Alignment can easily be converted to edit transcript and vice versa

For modeling standpoint they are quite different

edit transcript emphasizes the putative mutational events that transform one string to another

while alignment displays the relationship only

So, one is process (edit transcript), the other is the product(alignment)