PAAA: a progressive iterative alignment algorithm based on anchors

Authors:
Ahmed Mokaddem;Mourad Elloumi
Affiliations:
Higher School of Sciences and Technologies of Tunis, Tunisia;Higher School of Sciences and Technologies of Tunis, Tunisia
Venue:
PRIB'11 Proceedings of the 6th IAPR international conference on Pattern recognition in bioinformatics
Year:
2011

Citing 3
Cited 0

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Software note: MSAID: multiple sequence alignment based on a measure of information discrepancy

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Abstract

In this paper, we present a new iterative progressive algorithm for Multiple Sequence Alignment (MSA), called Progressive Iterative Alignment Algorithm Based on Anchors (PAAA). Our algorithm adopts a new distance, called anchor distance to compute the distance between two sequences, and a variant of the UPGMA method to construct a guide tree. PAAA is of complexity O(N4+N*L2) in computing time, where N is the number of the sequences and L is the length of the longest sequence. We benchmarked PAAA using different benchmarks, e.g., BALIBASE, HOMSTRAD, OXBENCH and BRALIBASE, and we compared the obtained results to those obtained with other alignment algorithms, e.g., CLUSTALW, MUSCLE, MAFFT and PROBCONS, using us criteria the Column Score (CS) and the Sum of Pairs Score (SPS). We obtained good results for protein sequences.