Overview of the ProDA algorithm

Copyright information:

Taken from "Multiple alignment of protein sequences with repeats and rearrangements"

Nucleic Acids Research 2006;34(20):5932-5942.

Published online 26 Nov 2006

PMCID:PMC1635250.

© 2006 The Author(s)

() Compute all-versus-all PLAs. () Identify possible repeats by computing non-overlapping PLAs. () Generate a block of possibly alignable regions from the PLAs. () Compute a guide tree for the block. () Progressively align sequences in the block and eliminate spurious alignments using heuristic filters. () Trim the block alignment. () Discard used PLAs, and repeat the alignment process until no more alignable blocks of length at least can be found. The end result is a set of aligned regions with length at least .