Neweyes: a system for comparing biological sequences using the running Karp-Rabin Greedy String-Tiling algorithm.
A system for aligning nucleotide or amino acid biosequences is described. The system, called Neweyes, employs a novel string matching algorithm. Running Karp-Rabin Greedy String Tiling (RKR-GST), which involves tiling one string with matching substrings of a second string. In practice, RKR-GST has a computational complexity that appears close to linear. With RKR-GST, Neweyes is able to detect transposed substrings or substrings of one biosequence that appears rearranged in a second sequence. Repeated substrings can also be detected. Neweyes also supports a form of matching-by-group that gives the effect of different amino acid mutation matrices. Neweyes can be used in a macro mode (searching a database for a list of biosequences that are similar to a given biosequence) or in a micro mode, where two biosequences are compared and more detailed output formats are available.
Wise
M J
MJ
Department of Computer Science, University of Sydney, Australia.
D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000235:genetics; D016208:Databases, Factual; D004815:Epidermal Growth Factor / Q000737:chemistry; D006801:Humans; D008969:Molecular Sequence Data; D009154:Mutation; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D016283:Proto-Oncogene Proteins p21(ras) / Q000737:chemistry; D012441:Saccharomyces cerevisiae / Q000235:genetics; D017386:Sequence Homology, Amino Acid
D011506:Proteins; D004815:Epidermal Growth Factor; D004247:DNA; C501009:HRAS protein, human; D016283:Proto-Oncogene Proteins p21(ras)