How to obtain or build Reference/BUSCO genes

[manighanipoor]

Hi,

I have a new genome assembly which was annotated with all annotation gff and fasta files. How can I create Reference/BUSCO genes in hmm format to put it in -b option?

[simonorozcoarias]

Hi! Thank you for your interest in MCHelper,

You can find the BUSCO reference genes in https://busco-data.ezlab.org/v5/data/lineages/ Look for the closest lineage to your interesting species. Then download the data, uncompress it and mix all the .hmm files contained in the hmm folder in one. Like this:

cat your_lineage_odb10/hmm/*.hmm > busco_genes.hmm

Please replace "your_lineage" with the correct one. Then you can use the busco_genes.hmm file in the -b option of MCHelper.

Best,

Simon O.

[manighanipoor]

Hi Simon,

Sorry for the late reply as I was on holiday. I greatly appreciate your help.

Cheers, Mani

On Fri, Dec 15, 2023 at 7:38 PM Simon Orozco-Arias @.***> wrote:

Hi! Thank you for your interest in MCHelper,

You can find the BUSCO reference genes in https://busco-data.ezlab.org/v5/data/lineages/ Look for the closest lineage to your interesting species. Then download the data, uncompress it and mix all the .hmm files contained in the hmm folder in one. Like this:

cat your_lineage_odb10/hmm/*.hmm > busco_genes.hmm

Please replace "your_lineage" with the correct one. Then you can use the busco_genes.hmm file in the -b option of MCHelper.

Best,

Simon O.

— Reply to this email directly, view it on GitHub https://github.com/GonzalezLab/MCHelper/issues/4#issuecomment-1857528335, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMUHZXMCJCKF6RGAV6CMDJLYJQHQPAVCNFSM6AAAAABAWDBNOOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJXGUZDQMZTGU . You are receiving this because you authored the thread.Message ID: @.***>

--

Mani Ghani poor Samami, PhD

Bioinformatics and Computational Genetics

School of Biological Sciences

The University of Adelaide

Adelaide, South Australia 5005

AUSTRALIA

Ph: +61 402196855

*Email: @.** **@.***>