# Bioinformatics

> Computational biological data analysis

- Skill: `ffsshhttiikk/bioinformatics` (Agent Skill)
- Install (CLI): `npx skillmds@latest add ffsshhttiikk/bioinformatics`
- Raw SKILL.md: https://api.skillmd.com/api/skills/ffsshhttiikk/bioinformatics/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- License: MIT
- Author: ffsshhttiikk (https://skillmd.com/u/ffsshhttiikk)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/ffsshhttiikk/bioinformatics

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## What I do

- Analyze and interpret large-scale biological datasets
- Perform sequence alignment and homology modeling
- Develop algorithms for biological data processing
- Create and maintain biological databases
- Predict protein structure and function
- Identify biomarkers and genetic variants

## When to use me

- When analyzing genomic, proteomic, or transcriptomic data
- When searching sequence databases (BLAST, FASTA)
- When predicting protein structure or function
- When identifying variants from sequencing data
- When building phylogenetic trees
- When analyzing gene expression patterns

## Key Concepts

### Sequence Analysis

**Alignment Algorithms**
- Needleman-Wunsch: Global alignment
- Smith-Waterman: Local alignment
- BLAST: Heuristic local alignment
- FASTA: Fast sequence similarity search

```python
# Example: Simple sequence alignment scoring
def simple_align(seq1, seq2, match=1, mismatch=-1, gap=-2):
    """Calculate simple alignment score."""
    score = 0
    for a, b in zip(seq1, seq2):
        if a == b:
            score += match
        else:
            score += mismatch
    return score
```

### Biological Databases

- NCBI (GenBank, PubMed, BLAST)
- UniProt: Protein sequences and function
- PDB: Protein structures
- Ensembl: Genome annotations
- UCSC Genome Browser

### Data Formats

- FASTA: Sequence data
- FASTQ: Sequences + quality scores
- SAM/BAM: Sequence alignment
- VCF: Variant calls
- PDB: Protein structure
- GO: Gene Ontology annotations