Contents
What is BPGA in biology?
Here we present an ultra-fast computational pipeline BPGA (Bacterial Pan Genome Analysis tool) with seven functional modules. The performance of BPGA has been evaluated using a dataset of complete genome sequences of 28 Streptococcus pyogenes strains.
How to install BPGA?
- On Windows: Install BPGA by simply double clicking on Installer file or extracting from zip. Open BPGA folder and change directory to bin folder.
- On Linux: Extract the files from tar.gz by command: tar -zxvf bpga-version-X-linux-xxx-xx.tar.gz. Open BPGA folder and change directory to bin folder.
What is the full form of BPGA?
Acronym. Definition. BPGA. Bulgarian Petroleum and Gas Association.
What is Bpg respiratory system?
2,3-Bisphosphoglycerate (BPG), also known as 2,3-Disphosphoglycerate (2,3-DPG), promotes hemoglobin transition from a high-oxygen-affinity state to a low-oxygen-affinity state.
How do I download from Usearch?
Install usearch for using in qiime
- 1) Download usearch5.2.236 and usearch6.1.
- http://www.drive5.com/usearch/download.html.
- 2) Rename files.
- 3) Move files to /usr/local/bin/ (Ubuntu/Linux)
- chmod a+x usearch usearch61.
- sudo mv usearch /usr/local/bin/
- sudo mv usearch61 /usr/local/bin/
What are pan bacteria?
Pan Bacteria 1 and Pan Bacteria 3 are designed to detect the broadest possible collection of bacteria involved in human biology. We began by designing assays against evolutionarily conserved regions of the 16S rRNA gene.
What are the features of the BPGA pipeline?
In addition to all types of analyses offered by currently available tools, this pipeline contains certain novel features like Exclusive Gene Family Analysis, KEGG Pathway Analysis, GC Content Analysis, Subset Analysis etc.
How is BPGA used in pan genome analysis?
In addition to the routine pan genome analyses, BPGA introduces a number of novel features for downstream analyses like core/pan/MLST (Multi Locus Sequence Typing) phylogeny, exclusive presence/absence of genes in specific strains, subset analysis, atypical G + C content analysis and KEGG & COG mapping of core, accessory and unique genes.
What kind of input files can BPGA process?
Three types of input files can be processed by BPGA: GenBank file: BPGA processes GenBank (.gbk) files for orthologous cluster analysis and generates an input file that may be used as an input for USEARCH, CD-HIT or OrthoMCL for clustering proteins.
When did BPGA consider more than one enzyme?
*In BPGA-1.3.0 or later, there is minor change in pathway calculations. It considers one enzyme involved in more than one pathways. Earlier versions used to consider one enzyme in only one pathway. Last update on 12/May/2017 : introduced pan profile plot with combinations from matrix input.