Constrained Multiple Sequence Alignment Tool with Tutorial Module

Abstract

Recently, the concept of Constrained Multiple Sequence Alignments was proposed to make it possible for biologists to incorporate their knowledge about the functionalities and structure of sequences in their alignments. It has been anticipated that constrained sequence alignment was to integrate the knowledge of biologists with regards to the structures/functionalities/consensuses of their data sets into sequence alignments such that specified residues matching the given constraints are aligned together in the result. The “Constrained Multiple Sequence Alignment Too! with Tutorial Module” is an online application which includes a Constrained Multiple Sequence Alignment Tool, the CMSA Database and the CMSA Tutorial Module. The CMSA Tool uses a memory-efficient CPSA algorithm in aligning two sequences and the progressive approach in aligning multiple sequences. Input validation provided by the CMSA ensures that the data processed by the server are correct. The CMSA Tool generates a text file that is available for the user to download. The CMSA Database allows users to browse through biological sequences, substitution matrices and CMSA results saved and managed by the CMSA Database Administrator. The Tutorial Module built with the CMSA Tool, allows the CMSA Lesson Administrator to update the text part of the lessons in the database, upload images that are important in letting the users understand the lessons and upload supplementary materials which the users can download. The Lesson Administrator can also update the quiz items per lesson, which will let the users assess how well they understood the lesson.