MeLanGE - Documentation

Snakemake python

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MeLanGE is an automated pipeline for the genomic annotation of a group of genomes, followed by the detection of the most important features to distinguish a group of genomes, as determined by a metadata label.

MeLanGE has two independent, but connected, components:

MeLanGE is implemented in a Snakemake workflow, thus contributing to reproducible and scalable data analysis.


1) Genome annotation

MeLanGE allows the quick annotation of a group of genomes with several databases and gives as final output formatted tables with the annotations per genome.
To get more information about the third-parties databases and tools that MeLanGE uses, please check the respective links and references.

1.1) Gene calling and general annotation

MeLanGE starts with gene calling performed with Prokka v1.14.5 [1]. Prokka provides several output files per genome, including .gbk and .faa files, which are made available and used in the following steps.

1.2) Functional annotation

Functional annotation is conducted with three databases: Pfam [2], COG [3] and KEGG [4].

Pfam

For the annotation using Pfam identifiers, a local database using HMMER v3.3 is constructed from the latest Pfam-A.hmm release, downloaded from the Pfam official website. Then, a hmmscan search is performed on all input genomes and the best hit per ORF (cut-off: -E 1e-5) is selected.

COG

To perform the annotation regarding Clusters of Orthologous Genes (COG), the cdd2cog v0.2 script was adapted. In summary, query proteins are blasted with RPS-BLAST+ (Reverse Position-Specific BLAST) function, from the blast+ v2.9.0 suite, against COGs database, implemented within NCBI’s Conserved Domain Database (CDD), and the best hit per ORF (cut-off: -E 1e-5) is selected.

KEGG

To obtain the KEGG Orthology (KO) identification of the proteins, the prokka2KEGG script was adapted. Here, previously annotated UniProtKB IDs by Prokka are converted into KO ids using a cross-reference database provided by UniProt.

1.3) Output files

  • Statistics.csv - % of Orfs annotated with each database.

  • for each database: counts, presence/absence (PA) and relative abundance tables.

  • Pfam_description.csv, Cog_description.csv, Kegg_description.csv - the mapping of the identified annotation with clans, names, descriptions, etc.

  • folder Orf_per_genome: each genome has a unique file containing all orfs identified by Prokka and the subsequent annotations with the four different databases.


2) Feature Selection

After the annotation step, MeLanGE offers the opportunity to identify the most important genome functions to distinguish genomes according to a category such as isolation source, environment characteristics, etc. Such mapping information should be mentioned in the medatata.csv file.

As a default, MeLanGE only performs the functional annotation pipeline. To also run the feature selection pipeline, substitute in config.yml for True to perform feature selection:

# --- Run Feature Selection (True or False)
FS: True

Future implementations

  • Improve report output.

Citing MeLanGE

For now, MeLanGE does not have a publication describing its functionalities (we are working on it). Please use a link to MeLanGE Github when you reference this tool.

MeLanGE Contributions

1 Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico da Universidade de Lisboa, Lisbon, Portugal
2 Associate Laboratory, Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
3 Department of Environmental Microbiology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany


Funding

This work was supported by the Portuguese Foundation for Science and Technology (FCT) through the research project PTDC/MAR-BIO/1547/2014 and by ‘Direção-Geral de Política do Mar’, Ministry of the Sea through the “Fundo the Azul” funding program of (grant number FA_05_2017_032). SGS is the recipient of a PhD scholarship conceded by FCT (PD/BD/143029/2018) and was supported by a FEMS-GO-2019-511 research and training grant conceded by the Federation of European Microbiological Societies (FEMS). Further support was provided from national funds through FCT in the scope of the projects UIDB/04565/2020 and UIDP/04565/2020 of the Research Unit Institute for Bioengineering and Biosciences - iBB and the project LA/P/0140/2020 of the Associate Laboratory Institute for Health and Bioeconomy - i4HB. UNR was funded by the Helmholtz Young Investigator grant VH-NG-1248 Micro “Big Data”.

References

  • [1] Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30(14):2068-9.
  • [2] Galperin MY, Kristensen DM, Makarova KS, Wolf YI, Koonin EV. Microbial genome analysis: the COG approach. Brief Bioinform. 2019;20(4):1063-70.
  • [3] Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar GA, Sonnhammer ELL, et al. Pfam: The protein families database in 2021. Nucleic Acids Res. 2020.
  • [4] Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28(1):27-30.