Scrutineer: a computer program that flexibly seeks and describes motifs and profiles in protein sequence databases

Area of Science:

• Bioinformatics
• Computational Biology
• Structural Bioinformatics

Background:

• Protein sequence databases are crucial for biological research.
• Efficient searching tools are needed to analyze vast amounts of protein data.
• Identifying motifs and patterns aids in understanding protein function and evolution.

Purpose of the Study:

• To introduce Scrutineer, an interactive program for motif and pattern searching in protein databases.
• To provide users with flexible and advanced search functionalities.
• To enable rapid identification of sequence features within large datasets.

Main Methods:

• Developed an interactive, user-friendly program named Scrutineer.
• Implemented capabilities for various search types including amino acid strings, variable-length segments, and delocalized constraints.
• Enabled searches within specific database subsets or sequence regions.
• Integrated secondary structure predictions and physicochemical characteristics into search criteria.
• Allowed combination of search criteria and use of aligned sequences as targets with weighting schemes.

Main Results:

• Scrutineer successfully searches Swissprot, PIR, and SeqDb protein sequence databases.
• Demonstrated rapid search times, locating hexamers in PIR release 22.0 (3.7 x 10^6 amino acids) in approximately 36 seconds.
• The program can describe databases, user-specified hits, and defined sequence regions.
• Source code and manual are freely distributed.

Conclusions:

• Scrutineer offers a powerful and efficient solution for protein sequence motif and pattern discovery.
• Its user-friendly interface and advanced features facilitate complex biological data analysis.
• Free distribution of Scrutineer promotes its accessibility and adoption in the scientific community.