PICS-Ord: Unlimited Coding of Ambiguous Regions by Pairwise Identity and Cost Scores Ordination

Background: We present a novel method to encode ambiguously aligned regions in fixed multiple sequence alignments by ‘Pairwise Identity and Cost Scores Ordination’ (PICS-Ord). The method works via ordination of sequence identity or cost scores matrices by means of Principal Coordinates Analysis (PCoA). After identification of ambiguous regions, the method computes pairwise distances as sequence identities or cost scores, ordinates the resulting distance matrix by means of PCoA, and encodes the principal coordinates as ordered integers. Three biological and 100 simulated datasets were used to assess the performance of the new method. Results: Including ambiguous regions coded by means of PICS-Ord increased topological accuracy, resolution, and bootstrap support in real biological and simulated datasets compared to the alternative of excluding such regions from the analysis a priori. In terms of accuracy, PICS-Ord performs equal to or better than previously available methods of ambi...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: Robert K. Luecking, Brendan P. Hodkinson, Alexandros Stamatakis, Reed A. Cartwright
• Keywords: Ambiguous Region, Artificial Intelligence, BMCBI 2011, Cost Scores, Sequence Alignment