STORM

STORM processes batches of protein sequences by extracting ORFs and performing BLAST and FASTA similarity searches, Pfam domain predictions, and ProtParam physicochemical calculations to support functional annotation and comparative analyses.

Key Features:

• Batch processing: Accepts and processes a batch file containing numerous protein sequences for high-throughput analysis.
• ORF prediction and extraction: Extracts protein sequences following open reading frame (ORF) prediction to identify viable coding regions.
• Web-based similarity searches (BLAST, FASTA): Runs BLAST and FASTA searches against known protein databases to identify homologs and infer function.
• Pfam domain prediction: Predicts conserved protein domains using Pfam to characterize functional motifs and structures.
• ProtParam physicochemical calculations: Computes molecular weight, amino acid composition, extinction coefficient, instability index, aliphatic index, and GRAVY using ProtParam.
• Integrated workflow: Integrates BLAST, FASTA, Pfam, and ProtParam analyses into a single processing workflow.
• Structured output: Organizes and summarizes analysis results into an Access database format for downstream use.

Scientific Applications:

• Genomic research: Supports large-scale analysis of protein sequences derived from genome projects.
• Gene annotation: Aids functional annotation of predicted genes through similarity searches and domain prediction.
• Functional genomics: Provides physicochemical and domain data to interpret protein function in genomic contexts.
• Proteomics: Supplies calculated properties relevant to protein stability, solubility, and experimental characterization.
• Evolutionary biology: Enables identification of homologs and conserved domains for evolutionary and comparative analyses.

Methodology:

Extract ORFs from input sequences, perform BLAST and FASTA similarity searches against protein databases, run Pfam domain predictions, calculate ProtParam properties (molecular weight, amino acid composition, extinction coefficient, instability index, aliphatic index, GRAVY), and export summarized results to an Access database.