dfast_core
DDBJ Fast Annotation and Submission Tool (by nigyta)
mantis
A package to annotate protein sequences (by PedroMTQ)
dfast_core | mantis | |
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2 | 6 | |
72 | 52 | |
- | - | |
6.3 | 3.1 | |
3 days ago | 5 months ago | |
Python | Python | |
- | MIT License |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
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.
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.
dfast_core
Posts with mentions or reviews of dfast_core.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-10-11.
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orfs in DNA
If you need more accurate ORF(CDS) prediction including functional annotation, I recommend using CLI tools such as prokka, bakta, or DFAST (DFAST is also available in a web version).
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Is there any other tool for COG annotation of the bacterial genome than EggNOG mapper?
reCOGnizer (https://github.com/iquasere/reCOGnizer) can annotate with COGs, and the other databases available at CDD. It obtains all information concerning COGs description and categories, and outputs krona plots and TSV tables in formats easy to analyze. There is also mantis (https://github.com/PedroMTQ/mantis), prokka (https://github.com/tseemann/prokka) and DFAST (https://github.com/nigyta/dfast_core), the latter two work on contigs and the first two are for proteins
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
What are some alternatives?
When comparing dfast_core and mantis you can also consider the following projects:
prokka - :zap: :aquarius: Rapid prokaryotic genome annotation
bakta - Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
Biopython - Official git repository for Biopython (originally converted from CVS)
Hail - Cloud-native genomic dataframes and batch computing