The accuracy of several multiple sequence alignment programs for proteins

Background: There have been many algorithms and software programs implemented for the inference of multiple sequence alignments of protein and DNA sequences. The "true" alignment is usually unknown due to the incomplete knowledge of the evolutionary history of the sequences, making it difficult to gauge the relative accuracy of the programs. Results: We tested nine of the most often used protein alignment programs and compared their results using sequences generated with the simulation software Simprot which creates known alignments under realistic and controlled evolutionary scenarios. We have simulated more than 30000 alignment sets using various evolutionary histories in order to define strengths and weaknesses of each program tested. We found that alignment accuracy is extremely dependent on the number of insertions and deletions in the sequences, and that indel size has a weaker effect. We also considered benchmark alignments from the latest version of BAliBASE and the ...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Paulo A. S. Nuin, Zhouzhi Wang, Elisabeth R. M. Tillier
• Keywords: Alignment Accuracy, BMCBI 2006, Sequence Alignment, Sequences