caa a22 4500 477067166 CHVBK 20180405111415.0 cr unu---uuuuu 170330e19960101xx s 000 0 eng 10.1007/BF02458279 doi (NATIONALLICENCE)springer-10.1007/BF02458279 Taylor William Division of Mathematical Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, NW7 1AA, London, UK aut A non-local gap-penalty for profile alignment [Elektronische Daten] [William Taylor] The length of an alignment of biological sequences is typically longer than the mean length of its component sequences. (This arises from the insertion of gaps in the alignment.) When such an alignment is used as a profile for the alignment of further sequences (or profiles), it will have a bias toward additional sequences that match the length of the profile, rather than the mean length of sequences in the profile, as the alignment of these well entail fewer (or smaller) insertions) so avoiding gap-penalties). An algorithm is described to correct this bias that entails monitoring the correspondence, for every pair of positions, of the mean separations in both profiles as they are aligned. The correction was incorporated into a standard dynamic programming algorithm through a modification of the gap-penalty, but, unlike other approaches, this modification is not local and takes into consideration the overall alignment of the sequences. This implies that the algorithm cannot guarantee to find the optimal alignment, but tests suggest that close approximations are obtained. The method was tested on protein families by measuring the area in the parameter space of the phase containing the correct multiple alignment. No improvement (increase in phase area) was found with a family that required few gaps to be aligned correctly. However, for highly gapped alignments, a 50% increase in area was obtained with one family and the correct alignment was found for another that could not be aligned with the unbiased method. Society for Mathematical Biology, 1996 Bulletin of Mathematical Biology Kluwer Academic Publishers 58/1(1996-01-01), 1-18 0092-8240 58:1<1 1996 58 11538 https://doi.org/10.1007/BF02458279 text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1007/BF02458279 text/html Onlinezugriff via DOI NATIONALLICENCE 100 1- Taylor William Division of Mathematical Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, NW7 1AA, London, UK aut NATIONALLICENCE 773 0- Bulletin of Mathematical Biology Kluwer Academic Publishers 58/1(1996-01-01), 1-18 0092-8240 58:1<1 1996 58 11538 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer