ys2ec_snakefiles

Snakemake snakefiles for making HHMs of yeast proteins and searching against custom-made ec_pep database using the HH-suite3 software suite.

One snakefile takes a multi-sequence FASTA as input.
In the other, you provide the standard yeast names before running the the snakefile with Snakemake.

This repo and the snakefiles herein accompany the Knutson laboratory publication Belkevich et al, 2023. (Details to be updated shortly.)

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Main supporting software

HH-suite3 reference:

Steinegger M, Meier M, Mirdita M, Vöhringer H, Haunsberger S J, and Söding J (2019) HH-suite3 for fast remote homology detection and deep protein annotation, BMC Bioinformatics, 473. doi: 10.1186/s12859-019-3019-7 PMID: 3152110

Snakemake reference:

Mölder, F., Jablonski, K.P., Letcher, B., Hall, M.B., Tomkins-Tinch, C.H., Sochat, V., Forster, J., Lee, S., Twardziok, S.O., Kanitz, A., Wilm, A., Holtgrewe, M., Rahmann, S., Nahnsen, S., Köster, J. (2021) Sustainable data analysis with Snakemake. F1000Res 10, 33. PMID: 34035898

Related

• My Repository for running command line-based HH-suite3 software in Jupyter environment provided via MyBinder Service
• My hhsuite3-utilities sub-repo