Alignments of multiple protein sequences are problemmatic both methodologically since most algorithms build from an initial pairwise alignment, as well as interpretationally. Most good alignments contain elements of both statistical fitness as well as functional interpretation. Most good alignments which originated from an algorithm have also received some manual adjustment. The PI completed an extensive alignment of 13 quite different aldehyde dehydrogenase sequences. This alignment was extensively adjusted manually. The objective of this allocation was to use this as a basis for evaluation of the suitability of the MSA and other alignment programs together with various scoring matrices and gap penalties. Alignments of this group of sequences using the MSA and Gotoh algorithms with variable gapping penalties has been instructive in illustrating the need to examine a variety of gapping parameters when constructing a multiple alignment with sequences of low (15-20%) ident ity, and the work can soon be written up for publication. Some additional units of C90 time may be needed for follow-up evaluations.
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