UPIMAPI
UniProt Id Mapping through API (by iquasere)
eggnog-mapper
Fast genome-wide functional annotation through orthology assignment (by eggnogdb)
| UPIMAPI | eggnog-mapper | |
|---|---|---|
| 3 | 1 | |
| 26 | 536 | |
| - | 3.5% | |
| 7.5 | 4.3 | |
| 5 months ago | 2 months ago | |
| Python | Python | |
| BSD 3-clause "New" or "Revised" License | GNU Affero General Public License v3.0 |
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.
UPIMAPI
Posts with mentions or reviews of UPIMAPI.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-05-26.
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Any programs/packages that will allow me to compare cluster annotations obtained from metagenomic data?
You may run MOSCA (https://github.com/iquasere/MOSCA), it performs all major steps of metagenomics analysis. It includes that functional classification you are looking for, since with UPIMAPI (https://github.com/iquasere/UPIMAPI) it annotates with UniProt DB as reference, and obtains information including taxonomy, EC numbers, and even those GOs, and reCOGnizer (https://github.com/iquasere/reCOGnizer), which annotates with CDD DB as reference, and obtains orthologous groups information (COG, Pfam, etc).
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Metatranscriptomics Workflow Questions?
Prediction of coding sequences takes as input the contigs you obtained, and gives you the translated genes. Besides annotating with the KEGG database, you may also want to annotate with more general purpose databases (e.g. UniProt), as these provide more taxonomies and functional information. MOSCA includes UPIMAPI (https://github.com/iquasere/UPIMAPI) and reCOGnizer (https://github.com/iquasere/reCOGnizer), which annotate genes with reference to UniProt and CDD databases using two different methods, providing complementary information. This is the same methodology used by widely popular tools such as eggNOG-mapper and Prokka, but these use other databases.
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Problems using Prokka
Install with mamba instead of conda, no more problems. Or use UPIMAPI (https://github.com/iquasere/UPIMAPI) together with reCOGnizer (https://github.com/iquasere/reCOGnizer), since these tools obtain better results when annotating proteins
eggnog-mapper
Posts with mentions or reviews of eggnog-mapper.
We have used some of these posts to build our list of alternatives
and similar projects.
What are some alternatives?
When comparing UPIMAPI and eggnog-mapper you can also consider the following projects:
ncbi-genome-download - Scripts to download genomes from the NCBI FTP servers
atlas - ATLAS - Three commands to start analyzing your metagenome data
goatools - Python library to handle Gene Ontology (GO) terms
Hail - Cloud-native genomic dataframes and batch computing
galaxy - Data intensive science for everyone.
deepvariant - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.