SynPAL — Synteny Informed Pathway Assembly & Layout

Overview

SynPAL maps metabolic pathway genes onto real genomic coordinates and measures how often they stay clustered — same replicon, same strand, within 2,000 bp — across species. Pathways whose arrangements are conserved are converted into gene-order recommendations and downloadable constructs (method,atlas,designs).

Data provenance

Pathway–enzyme mappings are BioCyc-derived aggregates; genomes are55 curated prokaryotes (one representative per species). All scores are computed withmethod v2 co-directional clustering (gap ≤ 2,000 bp) and exported as a static snapshot from reanalysis/database/synpal.db on2026-07-30. 7,225gene symbols are indexed for lookup.

Software

The analysis pipeline is provided as the synpalPython toolkit (reanalysis/ in the source repository); this website is a fully staticAstro build deployed on Cloudflare Pages — every JSON file under /data/ is directly downloadable. No accounts, no API keys, no server-side compute.

Limitations

• Gene matching is name-based (case-insensitive symbol), not sequence orthology — conserved ordercoverage is understated, and rare name collisions are possible.
• Conservation is descriptive: a conserved arrangement is an evolutionary precedent, not a guarantee of heterologous performance.
• All designs are in silico. Primers are a Wallace heuristic, not Primer3 output. Nothing here has been built or tested in the lab.