Journal: Microbiology Spectrum

Article Title: Phylogenomics analysis of velvet regulators in the fungal kingdom

doi: 10.1128/spectrum.03717-23

Figure Lengend Snippet: Comparison of the three characteristic motifs of velvet domains among the 21 major clades. The alignment of velvet domains was performed against the profile hidden Markov model of velvet domain PF11754 with 243 residues ( https://www.ebi.ac.uk/interpro/entry/pfam/PF11754/ ) and then subjected to WebLogo ( https://weblogo.threeplusone.com/ ) to generate sequence logos. In the logo, the total stack height represents the information content of residues at that position. The relative height of each residue in the stack is proportional to its frequency at the position, and the residues were sorted so that the most common one was on the top of the stack. The full sequence logos of velvet domains are provided in Fig. S4. The residues are colored according to their chemical properties, of which polar ones G, S, T, Y, and C are in green; neutral ones Q and N are in purple; basic ones K, R, and H are in blue; acidic ones D and E are in red; and hydrophobic ones A, V, L, I, P, W, F, and M are in black. The black balls at the bottom indicate the consensus dominant residues in the 21 clades, and the red balls indicate the other conserved residues revealed by the ConSurf analysis.

Article Snippet: First, multiple alignments of protein sequences within each clade were constructed using HMMER 3.1 ( http://hmmer.org/ ) against the profile velvet hidden Markov model ( https://www.ebi.ac.uk/interpro/entry/pfam/PF11754/ ) in InterPro ( ).

Techniques: Comparison, Sequencing, Residue

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:

Journal: BMC Bioinformatics

Article Title: Investigation of dirigent like domains from bacterial genomes

doi: 10.1186/s12859-022-04832-6

Figure Lengend Snippet: HMM Dirigent domain profile of Pfam PF03018 DIR family from available sequenced genomes

Article Snippet: Fig. 2 HMM Dirigent domain profile of Pfam PF03018 DIR family from available sequenced genomes Uniprot [ ], was used to retrieve links to other databases (notably Ensembl, Interpro and the NCBI) and therefore information relating DIRLs and bacteria (Additional file : Table S1).

Techniques: