If RNA metagenome sequence or transcriptosome raw data can be used for macrel analysis about macrel HOT 4 CLOSED

That's a good question, Aslangabriel99. We did not benchmark its use in transcriptomic data, however, the rationale says it is possible to extract AMP info from metaT.

Have on mind that it may work only for bacterial transcriptomics (no eukaryotes, splicing messes things up) and that is because the assembly tool of Macrel's choice is Megahit. A work around this issue is feeding Macrel with your contigs and after that, it should work as normal as for metaG, with prodigal predicting the genes - again prokaryotic genes. As it is transcriptomics, it is wise to exclude genes found in the antisense strands (so pay attention to the sense of the smORFs). Taking these measures should ensure pretty much decent results if any.

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You may find interesting the AMPSphere, a resource we put together with almost 1 million AMPs from more than 64k metaG and almost 100k genomes. Pay a visit to our website at: https://ampsphere.big-data-biology.org/

There you will be able to find several kinds of info for each AMP, their classification into families and their biochemical features. Information about their taxonomy and geographical distribution are also available. AMPs from 72 different habitats are compiled with extensive info and their gene sequences.

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Hi,

Your demand was already answered in the google discussion group for ampsphere-users, please pay a visit there. I am now closing this issue.

Best,
Celio

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