PT  - JOURNAL ARTICLE
AU  - Annabel Perry
AU  - Suzanne E. McGaugh
AU  - Alex C. Keene
AU  - Heath Blackmon
TI  - CaveCrawler: An interactive analysis suite for cavefish bioinformatics
AID  - 10.1101/2021.12.01.470856
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.12.01.470856
4099  - http://biorxiv.org/content/early/2021/12/03/2021.12.01.470856.short
4100  - http://biorxiv.org/content/early/2021/12/03/2021.12.01.470856.full
AB  - The growing use of genomics data in diverse animal models provides the basis for identifying genomic and transcriptional differences across species and contexts. Databases containing genomic and functional data have played critical roles in the development of numerous genetic models but are lacking for most emerging models of evolution. There is a rapidly expanding use of genomic, transcriptional, and functional genetic approaches to study diverse traits of the Mexican tetra, Astyanax mexicanus. This species exists as two morphs, eyed surface populations and at least 30 blind cave populations, providing a system to study convergent evolution. We have generated a web-based analysis suite that integrates datasets from different studies to identify how gene transcription and genetic markers of selection differ between populations and across experimental contexts. Results can be processed with other analysis platforms including Gene Ontology (GO) to enable biological inference from cross-study patterns and identify future avenues of research. Furthermore, the framework that we have built A. mexicanus can readily applied to other emerging model systems.Competing Interest StatementThe authors have declared no competing interest.