Software tools for motif and pattern scanning: program descriptions including a universal sequence reading algorithm.
Two programs, MOTIF and PATTERN, that scan sequences for matches to user-defined motifs and patterns of motifs based on identity and set membership are described. The programs use a simple and logical notation to define motifs, and may be used either interactively or by using command line parameters (suitable for batch processing). The two programs described also incorporate a simple, yet reliable, algorithm that automatically detects in which of six possible formats the sequence entry is written.
Cockwell
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Department of Biochemistry, School of Biochemical and Physiological Sciences, University of Southampton, UK.
Giles
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D000465:Algorithms; D000595:Amino Acid Sequence; D001483:Base Sequence; D010363:Pattern Recognition, Automated; D011381:Programming Languages; D012984:Software; D014584:User-Computer Interface