MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences

Abstract

Background: The rapid increase in the amount of protein and DNA sequence information available has become almost overwhelming to researchers. So much information is now accessible that high-quality, functional gene analysis and categorization has become a major goal for many laboratories. To aid in this categorization, there is a need for non-commercial software that is able to both align sequences and also calculate pairwise levels of similarity/identity.

Results: We have developed MatGAT (Matrix Global Alignment Tool), a simple, easy to use computer application that generates similarity/identity matrices for DNA or protein sequences without needing pre-alignment of the data.

Conclusions: The advantages of this program over other software are that it is open-source freeware, can analyze a large number of sequences simultaneously, can visualize both sequence alignment and similarity/identity values concurrently, employs global alignment in calculations, and has been formatted to run under both the Unix and the Microsoft Windows Operating Systems. We are presently completing the Macintosh-based version of the program.

Figure 1

Screen shot of the data input screen of MatGAT v2.0. Protein or DNA sequences in the FASTA format can be entered by hand into the data box, uploaded from a text file, or pasted into place. Several scoring matrices are available for analyses: BLOSUM50, BLOSUM62, and PAM250. Additionally, "First Gap" and "Gap Extension" conditions may be altered for optimal alignment. The "Clear" button will delete the input sequence data and alignments, while leaving the matrix output unaffected until new data are analyzed.

Figure 2

Screen shot of MatGAT v2.0 output running under Windows XP. Aprotein data set is analyzed by MatGAT. The upper matrix contains the identity of the data set and the lower is the similarity. The inset screen contains a pop-up window generated by clicking on the sequence pair of interest; this window displays the pairwise alignment of the tomato and soybean protein sequences. The "Save All" button saves all the alignments into a text file, while the "Save Selected" button is enabled once you select one of the alignments for display. This button will selectively save all the alignments that you have chosen to view.

Figure 3

Screen shot of the Configuration Window of MatGAT v2.0. The colors of data output may be controlled from this screen, as well as configuration of Excel recognition by MatGAT.