This repository contains files and scripts to generate analysis and figures in the manuscript A catalogue of small proteins from the global microbiome:
Yiqian Duan, Celio Dias Santos-Junior, Thomas Sebastian Schmidt, Anthony Fullam, Breno L. S. de Almeida, Chengkai Zhu, Kuhn Michael, Xing-Ming Zhao, Peer Bork, Luis Pedro Coelho bioRxiv 2023.12.27.573469; doi: https://doi.org/10.1101/2023.12.27.573469
The results Global Microbial SMORFs Catalogue (GMSC) is available at https://gmsc.big-data-biology.org
The folder Resource_Generation contains scripts to generate the GMSC resource from raw data. Note that this requires downloading all the contigs from SPIRE and ProGenomes v2 as well as very large computational resources. The scripts are provided for transparency and reproducibility, but we recommend using the precomputed data (deposited at Zenodo or included here, see below) and the GMSC resource at https://gmsc.big-data-biology.org.
The folder Manuscript_Analysis contains pre-computed files and scripts to run the analysis and generate figures included in the GMSC manuscript. The scripts are written in Python (depenencies listed below). Generally speaking, these do not require large computational resources and interested users can run them on their own machines and adapt them to perform follow-up analyses.
The following are required for the scripts (other versions may work, we list the ones that were used).
| Software | Availability |
|---|---|
| NGLess (v.1.3.0) | https://github.com/ngless-toolkit/ngless |
| Prodigal (v 2.6.3) | https://github.com/hyattpd/Prodigal |
| Macrel (v.0.5) | https://github.com/BigDataBiology/macrel |
| JUG (v.2.1.1) | https://github.com/luispedro/jug |
| MMseqs2 | https://github.com/soedinglab/MMseqs2 |
| Swipe (v.2.1.1) | https://github.com/torognes/swipe |
| DIAMOND (v.2.0.4) | https://github.com/bbuchfink/diamond |
| HMMer (v.3.3.2) | https://hmmer.org/ |
| MAFFT (v.7.475) | https://mafft.cbrc.jp/alignment/software/ |
| RNAcode (v.0.3) | https://github.com/ViennaRNA/RNAcode |
| BWA (v.0.7.17) | https://github.com/lh3/bwa |
| BLAST (v.2.13.0) | https://blast.ncbi.nlm.nih.gov/Blast.cgi |
| TMHMM (v.2.0) | https://services.healthtech.dtu.dk/services/TMHMM-2.0/ |
| SignalP (v.5.0) | https://services.healthtech.dtu.dk/services/SignalP-5.0/ |
These databases are used in the construction and analysis of the catalogue.
| Database | Availability |
|---|---|
| SPIRE | https://spire.embl.de |
| ProGenomes v2 | https://progenomes2.embl.de/ |
| AntiFam (v.7.0) | ftp://ftp.ebi.ac.uk/pub/databases/Pfam/AntiFam/ |
| PRIDE | https://www.ebi.ac.uk/pride/ |
| RefSeq | https://ftp.ncbi.nlm.nih.gov/refseq/release/ |
| The Conserved Domain Database | https://ftp.ncbi.nih.gov/pub/mmdb/cdd |
| GTDB R95 | https://gtdb.ecogenomic.org/ |
smORF catalogue & annotations: The smORF catalogue and its annotations are available at https://doi.org/10.5281/zenodo.7944370
Preprocessed data: For convenience, the preprocessed files are available under the Manuscript_anlysis/data folder.