scientific-sequence-analysis

What problem does it solve?

DNA, RNA, and protein sequence analysis often requires performing multiple disparate tasks—composition analysis, codon usage, sequence alignment, and basic phylogenetics—in a reproducible workflow. This Skill provides a self-contained pipeline to streamline these analyses on small to medium sequence datasets, enabling researchers to derive meaningful insights with minimal setup.

Core Features & Use Cases

• Sequence composition analysis for DNA/RNA/protein sequences, including GC content and base/protein composition.
• Codon usage metrics (RSCU, CAI) and translation considerations for studying bias and expression potential.
• Pairwise and global alignment capabilities (Needleman-Wunsch/Smith-Waterman) with reusable utilities.
• Phylogenetic analysis options (distance-based metrics like Jukes-Cantor and clustering via UPGMA).
• ORF search, CpG island detection, and basic protein-property predictions (molecular weight, hydrophobicity) for small-scale genomic investigations.
• Use Case: Assess codon bias in a gene family, align conserved regions, and infer a rough phylogeny for a set of sequences.

Quick Start

Provide a DNA or protein sequence to obtain composition, codon usage metrics, alignments, phylogeny, ORFs, CpG islands, and protein properties.