Journal: Molecular Systems Biology

Article Title: Identification of novel toxins associated with the extracellular contractile injection system using machine learning

doi: 10.1038/s44320-024-00053-6

Figure Lengend Snippet: List of EAT candidates tested and their cytotoxicity.

Article Snippet: According to InterPro databases, the DUF4365 Hidden Markov Model (HMM) has a conserved peptide motif DxGxD...QxK.

Techniques:

Journal: bioRxiv

Article Title: METAWORKS: A flexible, scalable bioinformatic pipeline for multi-marker biodiversity assessments

doi: 10.1101/2020.07.14.202960

Figure Lengend Snippet: The pipeline can be run in a conda environment, providing raw paired-end Illumina reads, a configuration file, and a snakefile. Snakemake can be directed to run parallel jobs across many CPUs in a high performance computing environment. A summary of the steps carried out in the pipeline are shown in the dashed box. The standard pipeline is shown along with the variation needed to process ITS sequences (orange) and the variations needed to screen out putative pseudogenes (green). We note with the asterisk that the pseudogene removal step is currently different for rbcL and COI: for rbcL, longest ORF lengths are screened for outliers; whereas for COI, longest ORFs are further subjected to hidden Markov model (HMM) profile analysis and HMM scores are used to screen for outliers. For each exact sequence variant (ESV), for each sample, read counts and taxonomic assignments are provided along with bootstrap support values. An example of the taxonomic assignment output is shown in the table.

Article Snippet: Updates to MetaWorks will be made as needed to reflect advances in the underlying programs, reference databases, or hidden Markov model (HMM) profiles for pseudogene filtering.

Techniques: Sequencing, Variant Assay

Journal: bioRxiv

Article Title: METAWORKS: A flexible, scalable bioinformatic pipeline for multi-marker biodiversity assessments

doi: 10.1101/2020.07.14.202960

Figure Lengend Snippet: Input and output files are shown as parallelograms. Snakemake rules or processes are shown as ovals. The final results file contains ESVs, for each sample, as well as ESV/ORF sequences, read counts, as well as taxonomic assignments with bootstrap support values. The main dataflow is shown in black, if pseudogene filtering is selected these steps are shown in green, if pseudogene filtering is not selected the dashed steps are performed. The generation of various statistical reports are shown in grey.

Article Snippet: Updates to MetaWorks will be made as needed to reflect advances in the underlying programs, reference databases, or hidden Markov model (HMM) profiles for pseudogene filtering.

Techniques: