A fixed-point alignment technique for detection of recurrent and common sequence motifs associated with biological features.

A fixed-point alignment analysis technique is presented which is designed to locate common sequence motifs in collections of proteins or nucleic acids. Initially a program aligns a collection of sequences by a common sequence pattern or known biological feature. The common pattern or feature (fixed-point) may be a user-specified sequence string or a known sequence position like mRNA start site, which may be taken directly from the annotated feature table of GenBank. Once all alignment markers are located, the sequences are scanned for occurrences of given oligomers within a specified span both upstream and downstream of the fixed-point. The occurrences may then be plotted as a function of the position relative to the fixed-point, displayed as an actual sequence alignment or selectively summarized via various program options. Applications of the technique are discussed.