A major component approach to presenting consensus sequences.
BACKGROUND
Summarizing and displaying the information contained in a set of aligned sequences is an important aid to identifying patterns within the sequences. A variety of forms of consensus sequences have been used previously to provide this information. However, these methods can cause a loss of information or introduce ambiguities into the consensus sequence, and some graphical approaches may become difficult to interpret due to visual distortion.


RESULTS
We have developed a method to present a more precise and graphically clear view of a consensus sequence by using an approach based on defining the major components at each position in a sequence set. The major components are given in an ordered list and their frequencies are shown as histograms which can be colour coded to reflect conservative groupings. Minor components, a one-line character-based consensus sequence and information statistics can also be presented. As well as identifying the dominant sources of variation and conservation in the sequence set, the method also enables similarities and differences between subgroups of a sequence set to be readily assessed. AVAILIABILITY: On request from the authors.


BACKGROUND
bcsmith@usthk.ust.hk, hxue@usthk. ust.hk
Smith
D K
DK
Biochemistry Department, Hong Kong University of Science and Technology, Kowloon, Hong Kong.
Xue
H
H
D000595:Amino Acid Sequence; D001483:Base Sequence; D019295:Computational Biology; D016384:Consensus Sequence; D004722:Endoribonucleases / Q000235:genetics; D007135:Immunoglobulin Variable Region / Q000235:genetics; D007146:Immunoglobulin lambda-Chains / Q000235:genetics; D008969:Molecular Sequence Data; D012313:RNA / Q000235:genetics; D016337:RNA, Catalytic / Q000235:genetics; D018079:Receptors, GABA / Q000235:genetics; D011978:Receptors, Nicotinic / Q000235:genetics; D043262:Ribonuclease P; D016415:Sequence Alignment; D012984:Software
D007135:Immunoglobulin Variable Region; D007146:Immunoglobulin lambda-Chains; D016337:RNA, Catalytic; D018079:Receptors, GABA; D011978:Receptors, Nicotinic; D012313:RNA; D004722:Endoribonucleases; D043262:Ribonuclease P