IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments

Abstract

IVisTMSA is a software package of seven graphical tools for multiple sequence alignments. MSApad is an editing and analysis tool. It can load 409% more data than Jalview, STRAP, CINEMA, and Base-by-Base. MSA comparator allows the user to visualize consistent and inconsistent regions of reference and test alignments of more than 21-MB size in less than 12 seconds. MSA comparator is 5,200% efficient and more than 40% efficient as compared to BALiBASE c program and FastSP, respectively. MSA reconstruction tool provides graphical user interfaces for four popular aligners and allows the user to load several sequence files at a time. FASTA generator converts seven formats of alignments of unlimited size into FASTA format in a few seconds. MSA ID calculator calculates identity matrix of more than 11,000 sequences with a sequence length of 2,696 base pairs in less than 100 seconds. Tree and Distance Matrix calculation tools generate phylogenetic tree and distance matrix, respectively, using neighbor joining% identity and BLOSUM 62 matrix.

Keywords: FASTA; MSA Identity Matrix; MSA comparator; MSA editing tool.

Figure 1

Main interface of IVisTMSA. This provides links to start the seven tools of IVisTMSA. The specific tool can be run by clicking the respective link.

Figure 2

DnC approach used in various tools of IVisTMSA. In the first step an alignment is divided into subalignments (A). In the second step, Java threads are generated to perform various types of computations on the sub-MSAs and at the end the main thread performs the final computations (B).

Figure 3

Alignment-rendering model of IVisTMSA. The rendering model acts as an intermediary object between the input alignment and alignment displaying interface and manages loading, viewing, and editing of alignment efficiently.

Figure 4

Features provided by MSApad. It allows the user to save an alignment, find a residue/sequence name, add a sequence at any position in the alignment, move sequence up or down (A), calculate phylogenetic tree, conserved or consensus sequence, identity (with gaps or without gaps), set color of an alignment using six color schemes (B), and view and analyze protein 3D chemical structure and phylogenetic tree (C).

Figure 5

Consistent and inconsistent regions of the reference and test alignment. When the user selects a test file from the window displaying SPS and CS (A), a new interface showing consistency of test and reference alignment (B) is loaded. The consistent residues are shown in blue color, whereas inconsistent elements are displayed in grey color.