Fig. 1. An example of MSAID alignment. Twenty-three proteins come from four families, share three conserved motifs. The residues underlined are annotated as core blocks in BAliBASE. This alignment belongs to BAliBASE category 3 (multiple protein families).

Comparison of MSAID with two other iteratively progressive multiple sequence alignment methods

‘Method’ indicates the name of technique being evaluated, while columns indicating ‘References 1–5’ stand for the five reference categories of BAliBASE; numbers in parentheses indicate the number of alignments in a category. The average accuracy of each method across all 142 test alignments is shown in column ‘Total’. Bold numbers indicate the best accuracies obtained in each alignment category (columns indicating ‘References 1–5’ and ‘Total’). It can be seen that accuracy scores for MSAID are clearly better than the accuracies for two other techniques in all alignment categories studied. This is not surprising because MSAID utilizes much richer sequence information than MultAlin and IPMSA do.

Comparison of MSAID with five other multiple sequence alignment methods

‘Method’ indicates the name of technique being evaluated while ‘References 1–5’ stand for the five reference categories of BAliBASE; numbers in parentheses indicate the number of alignments in a category. The average accuracy of each method across all 142 test alignments is shown in column ‘Total 1’, while column ‘Total 2’ shows the average accuracy across the five BAliBASE categories (unweighted). Bold numbers indicate the best accuracies obtained in each alignment category (columns indicating ‘References 1–5’ as well as ‘Total 1’ and ‘Total 2’). It can be seen that MSAID consistently tends to perform as well or better than other methods. Albeit T-Coffee appears to be clearly superior to other methods in reference category Reference 4, while Muscle gets the highest score in category Reference 5; both kinds of average accuracies (as well as accuracies for reference categories: columns indicating ‘References 1–3’) are the highest for MSAID.