Alineator WEB server 2006

Abstract

This is a web server to show the behaviour of the Needleman and Wunsch (global) and Smith and Waterman (local) alignment algorithms. Students in this small project are suposed to be able to implement a functional version of both algorithms. The implementation of them is an excellent opportunity to understand the basic mechanisms to perform optimal pairwise alignments. Moreover, the web server can be simply used to explain the dynamic programming paradigm to beginner students in bioinformatics.

Input

Please, input the 2 FASTA sequences to perform a global/local alignment:

SEQUENCE 1
>NP_000362 MASHRLLLLCLAGLVFVSEAGPTGTGESKCPLMVKVLDAVRGSPAINVAVHVFRKAADDTWEPFASGKTS ESGELHGLTTEEEFVEGIYKVEIDTKSYWKALGISPFHEHAEVVFTANDSGPRRYTIAALLSPYSYSTTA VVTNPKE

Upload the file A

SEQUENCE 2
>NP_036813 MASLRLFLLCLAGLIFASEAGPGGAGESKCPLMVKVLDAVRGSPAVDVAV KVFKRTADGSWEPFASGKTAESGELHGLTTDEKFTEGVYRVELDTKSYWK ALGISPFHEYAEVVFTANDSGHRHYTIAALLSPYSYSTTAVVSNPQN

Upload the file B

Maximum accepted file size: 1500 bps or 1500 amino acids

Options

ALIGNMENT TYPE

Global
Local

Please select the substitution matrix

BLOSUM62
PAM120
DNA (symmetrical)
DNA (asymmetrical)

Gap penalty:

Display the similarity matrix

Bibliography

A general method applicable to the search for similarities in the amino acid sequence of two proteins.
Needleman SB and Wunsch CD. J Mol Biol. 1970 Mar;48(3):443-53.

Identification of common molecular subsequences.
Smith TF and Waterman MS. J Mol Biol. 1981 Mar 25;147(1):195-7.

Author

The alineator ^server is an application for educational purposes. The main objective is to show the students in a friendly and easy form how the basic forms of alignments are computed. The alineator program implements the Needleman and Wunsch (1970) algorithm and the Smith and Waterman (1981) algorithm.

The source code of the program in C is kindly provided under GPL license by the author upon request .

Version 1 of alineator^server has been written by Enrique Blanco

GENOME BIOINFORMATICS RESEARCH LAB