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.
