[1]: 440 These scientists were driven by the desire to solve the problem that many investigators face during studies that involve genomics and proteomics.
[2]: 7 Homologous genes could only be studied effectively using search tools that established like portions or local placement between two proteins or nucleic acid sequences.
BLAST makes an improvement to this technique by establishing brief, precise seed matches that it later joins up to form longer alignments.
[5]: 737 However, when dealing with lengthy sequences, the above-mentioned techniques are extremely sluggish and required considerable memory sizes.
All the above-mentioned problems necessitate the development of a fast reliable tool that can handle all types of sequences efficiently without consuming too many resources in a computer.
Large seeds are unable to find isolated homologies, whereas small ones generate numerous arbitrary hits that delay computation.
The first stage in PatternHunter analysis entails a filtering phase where the program hunts for matches in k alternating points as denoted by the most advantageous pattern.
However, there are plans to improve PatternHunter to attain the high sensitivity of the Smith - Waterman tool while obtaining BLAST pace.