mantis
A package to annotate protein sequences (by PedroMTQ)
refdb_generator
Automated creation of a few different HMM and diamond reference (by PedroMTQ)
| mantis | refdb_generator | |
|---|---|---|
| 6 | 1 | |
| 51 | 4 | |
| - | - | |
| 3.1 | 0.0 | |
| 4 months ago | about 2 years ago | |
| Python | Python | |
| MIT License | MIT License |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
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Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
mantis
Posts with mentions or reviews of mantis.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2021-11-15.
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database for protein biological function association
You could use https://github.com/PedroMTQ/mantis
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How to get consensus annotations for a de novo orthogroup/ortholog analysis?
https://github.com/PedroMTQ/mantis Mantis works on protein level but it does address the consensus matter you mentioned
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Is there any other tool for COG annotation of the bacterial genome than EggNOG mapper?
Hello, I'm the developer of Mantis (https://github.com/PedroMTQ/mantis). Mantis doesn't use a database for COGs specifically but it does output some of the IDs you mentioned (e.g., KOs, COGs). If this is important for your work I could consider creating a COG centric database (or at least format it to be natively compatible with Mantis). Anyhow, please check the GitHub page and message me or post an issue and I'll try to help out.
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Functional annotation of prokaryotic genomes
Thanks a lot! Will definitely try it out. Another question: Does Mantis+eggNOG annotate the genes with eggNOG-ortholog-ids? More generally, what are the resulting annotation types? (pfam, GO, KO, EC and description are listed, how about KR, BiGG, brite and cazy?)
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How can I map KEGG gene categories onto aligned genomes?
You could accomplish this by gene calling with prodigal and then annotating with a tools like Mantis https://github.com/PedroMTQ/mantis
refdb_generator
Posts with mentions or reviews of refdb_generator.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2021-10-20.
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Functional annotation of prokaryotic genomes
atm BIGG is not linked to any of the databases, but I do have another repo with BIGG genes (diamond DB) and BIGG reactions (HMMs). You could then just add these to the mantis config file (see here how) and use them alongside the other references.
What are some alternatives?
When comparing mantis and refdb_generator you can also consider the following projects:
prokka - :zap: :aquarius: Rapid prokaryotic genome annotation
Biopython - Official git repository for Biopython (originally converted from CVS)
Hail - Cloud-native genomic dataframes and batch computing