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Open Access Software

Multiple structure alignment with msTALI

Paul Shealy and Homayoun Valafar*

Author Affiliations

Department of Computer Science and Engineering, University of South Carolina, 315 Main Street, Columbia, SC 29208, USA

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BMC Bioinformatics 2012, 13:105  doi:10.1186/1471-2105-13-105

Published: 20 May 2012

Additional files

Additional file 1:

The C++ Source code for msTALI. The README file contains brief compilation and execution instructions.

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Additional file 2:

Table S1. Full alignment of the mobile domains of DNA polymerase obtained from the STAMP analysis software. Table S2: Full alignment for mobile domains of DNA polymerase from MATT. Table S3: Full alignment for mobile domains of DNA polymerase from msTALI. Table S4: Configuration for study of Polymerase structures based on backbone torsion angles. All parameters not listed have zero values. Table S5: A comparison of the domains from 1.10.150.20 that were divided by msTALI into two separate clusters. The larger cluster contains 27 domains (84% of the total domains), while the smaller cluster contains 5 domains (16%). Each domain from the smaller cluster was compared to a randomly selected domain from the larger cluster using SSAP. Domains from the small cluster are on the left (Domain 1), while domains from the large cluster are on the right (Domain 2). These comparisons were performed to validate msTALI’s results, ensuring that this division was not related to an anomaly in msTALI. Table S6: Parameters of msTALI for core identification. All parameters not listed have zero values. Table S7: Parameters of msTALI for identification for flexible structure alignment. All parameters not listed have zero values. Figure S1: Per-residue score of msTALI for the three DNA polymerase proteins 1KTQ, 2KTQ and 3KTQ. Residues with scores more than 3s outside of the mean score were identified as the hinge regions.

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