reCOGnizer Alternatives

reCOGnizer reviews and mentions

• Is there a way to achieve a similar COG annotation for Haloferax mediterranei?
  1 project | /r/bioinformatics | 10 Apr 2023
  1 project | /r/proteomics | 10 Apr 2023

  reCOGnizer (https://github.com/iquasere/reCOGnizer) will do that for you. It also outputs the COG categories in a krona plot

• Why do some HMMs come with a separate score table instead of embedding in as cut_ga, cut_tc, or cut_nc?
  1 project | /r/bioinformatics | 19 Jun 2022

  What tool are you using for analyzing them? Using something like reCOGnizer (https://github.com/iquasere/reCOGnizer) gives you the bitscores and evalues in a TSV table, next to the matches

• Metadbgwas, my tool ! What could I do better ?
  3 projects | /r/bioinformatics | 1 Jun 2022

  Finally, a huge help on developing is having a Continuous Integration/Deployment on the tool. CD refers to the conda suggestion above, as your tool would be readily available in a controlled environment. CI could use the GitHub Actions functionality provided by GitHub. You can see an example here

• 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

• How would you name the program that does cog annotation?
  1 project | /r/AskReddit | 11 Mar 2022

  I think reCOGnizer is a nice name

• Is there any other tool for COG annotation of the bacterial genome than EggNOG mapper?
  5 projects | /r/bioinformatics | 15 Nov 2021

  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

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  www.saashub.com | 10 May 2024

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