UPIMAPI Alternatives

Similar projects and alternatives to UPIMAPI based on common topics and language

MOSCA

12 32 8.2 Python UPIMAPI VS MOSCA

Meta-Omics Software for Community Analysis (by iquasere)
reCOGnizer

9 24 7.4 HTML UPIMAPI VS reCOGnizer

A tool for domain based annotation with databases from the Conserved Domains Database
WorkOS

workos.com sponsored

The modern identity platform for B2B SaaS. The APIs are flexible and easy-to-use, supporting authentication, user identity, and complex enterprise features like SSO and SCIM provisioning.
ncbi-genome-download

4 887 5.7 Python UPIMAPI VS ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers
eggnog-mapper

1 531 4.3 Python UPIMAPI VS eggnog-mapper

Fast genome-wide functional annotation through orthology assignment
atlas

2 346 9.3 Python UPIMAPI VS atlas

ATLAS - Three commands to start analyzing your metagenome data (by metagenome-atlas)
Biopython

31 4,167 9.6 Python UPIMAPI VS Biopython

Official git repository for Biopython (originally converted from CVS)
deepvariant

5 3,078 9.1 Python UPIMAPI VS deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
InfluxDB

www.influxdata.com sponsored

Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

NOTE: The number of mentions on this list indicates mentions on common posts plus user suggested alternatives. Hence, a higher number means a better UPIMAPI alternative or higher similarity.

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UPIMAPI reviews and mentions

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.

Any programs/packages that will allow me to compare cluster annotations obtained from metagenomic data?
3 projects | /r/bioinformatics | 26 May 2022

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).
Metatranscriptomics Workflow Questions?
4 projects | /r/bioinformatics | 24 May 2022

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.
Problems using Prokka
2 projects | /r/bioinformatics | 29 Mar 2022

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
A note from our sponsor - WorkOS
workos.com | 29 Apr 2024

The APIs are flexible and easy-to-use, supporting authentication, user identity, and complex enterprise features like SSO and SCIM provisioning. Learn more →