ANN: Macrel 1.4.0

[Luis Pedro Coelho]

Dear List,

We released Macrel 1.4.0! The big new feature is that it can use the AMPSphere API to match peptides to the AMPSphere database. You can install/update using conda (conda install bioconda::macrel)

It adds the query-ampsphere subcommand. For example, to get exact matches in the AMPSphere (identical peptide sequences):

macrel query-ampsphere \

    --fasta example_seqs/pep8.faa \

    --output out_ampsphere

To run mmseqs which allows for fuzzy matches:

macrel query-ampsphere \

    --fasta example_seqs/pep8.faa \

    --query-mode mmseqs \

    --output out_ampsphere

(You can also pass hmmer to get HMMER results which are family-level)

If you do use the results of this feature, please cite the AMPSphere paper as reference.

Right now, this uses the API, so makes calls to the same service that is running https://ampsphere.big-data-biology.org/ and requires internet access. It is also not very scalable if you have 1,000s of sequences.

 

FUTURE PLANS

I am in the process of adding support for local running (where macrel will download the right files first and then call the tools for you). The code currently available on github already works for exact & mmseqs. You run it with the same interface, just adding the --local flag

Part of the reason to add this functionality to macrel (instead of a separate tool) is that this could also be integrated into the prediction functionalities, so that it also in the cards, but probably not for the next release.

Bug reports and comments are appreciated!

Best, Luis

Luis Pedro Coelho | Queensland University of Technology | https://luispedro.org

https://orcid.org/0000-0002-9280-7885