comparative-genomics-comparative-annotation-projection

comparative-genomics-comparative-annotation-projection is a Bioinformatics & life sciences skill for AI agents, published by swaruplab in the operon repository on GitHub. Skillspace rates comparative-genomics-comparative-annotation-projection C (79/100) and it passed the safety scan; the rating is based on static analysis only.

Project gene annotations across genomes using TOGA (Kirilenko 2023 whole-genome-alignment chain-based projection with intactness classification), CESAR 2.0 (Sharma & Hiller 2017 codon-aware exon projection), LiftOff (Shumate & Salzberg 2020 reference-based annotation transfer), Liftover (UCSC), GeMoMa (Keilwagen 2019 evidence-based projection), and Comparative Annotation Toolkit (CAT). Use when transferring annotations from a well-annotated reference to query genome(s), classifying gene-loss vs gene-intact across many genomes at scale, building Zoonomia-style comparative annotations across hundreds of mammals or birds (Kirilenko 2023), detecting pseudogenization, projecting alternative isoforms, or selecting between WGA-anchored (TOGA) vs ortholog-based (LiftOff) annotation transfer strategies.

Grade

C

Quality

79 / 100

Safety

Passed

GitHub stars

90

Unproven: rated by static analysis only, not yet compared head-to-head.

Not launch-quality. It is graded C with a clean safety verdict, but our quality filters exclude it: it is a near-duplicate variant of another skill. So it is not in our launch-quality set, the skills our MCP server searches and recommends. How launch-quality is decided

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