Request for chain file generation: Drosophila melanogaster (dm6) and Rhodnius prolixus (RproC3)

[María José Delgado]

Dear UCSC Genome Browser Team,

I'm a PhD student currently conducting comparative genomic analyses between Drosophila melanogaster and Rhodnius prolixus. To perform cross-species coordinate conversion (liftOver) and whole-genome alignments, I would like to kindly request your assistance in generating pairwise alignment chain files between the following two assemblies:

1. Drosophila melanogaster – dm6 / BDGP Release 6 (GCA_000001215.4)

2. Rhodnius prolixus – RproC3 / Rhodnius_prolixus-3.0.3 (GCA_000181055.3)
   Available at NCBI: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_000181055.3/
   Also available through VectorBase (VEuPathDB): https://vectorbase.org/vectorbase/app/record/dataset/DS_4f4c90a272

Ideally, I would appreciate chain files in both directions (dm6 → RproC3 and RproC3 → dm6), however, even a single direction would be of great value for our analyses.

Please let me know if you need any additional information or if the Rhodnius prolixus assembly requires any specific format for processing.

Thank you very much for your time and consideration.

Best regards,
María José Delgado
Centro de Bioinvestigaciones - UNNOBA, Argentina
majo...@gmail.com

[Gerardo Perez]

Hello, María José.

Thank you for your interest in the Genome Browser.

We have made the requested liftOver chain files available on our download server:

dm6 -> GCA_000181055.3: https://hgdownload.soe.ucsc.edu/goldenPath/dm6/liftOver/dm6ToGCA_000181055.3.over.chain.gz

GCA_000181055.3 -> dm6: https://hgdownload.soe.ucsc.edu/hubs/GCA/000/181/055/GCA_000181055.3/liftOver/GCA_000181055.3ToDm6.over.chain.gz

I hope this is helpful. If you have any questions or need further assistance, please feel free to reach out to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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[María José Delgado]

Dear Gerardo,

Thank you very much for generating the chain files so promptly, they have been extremely helpful for our analyses.

I would like to take this opportunity to request an additional set of chain files, this time between Drosophila melanogaster and Tribolium castaneum:

1. Drosophila melanogaster – dm6 / BDGP Release 6 (GCA_000001215.4)

2. Tribolium castaneum – Tcas5.2 (GCA_000002335.3)
   Available at NCBI: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_000002335.3/

As before, I would greatly appreciate chain files in both directions (dm6 → Tcas5.2 and Tcas5.2 → dm6), although a single direction would already be of great value.

Please let me know if you need any additional information.

Thank you again for your time and support.

Best regards,
María José Delgado