pOmpR promoter

Author

Samuel Ortion

Published

September 24, 2023

In registry

Only three BBa_R regulatory type parts registered as gathered by an extensive Google search. May be other parts remains in other part types.

the BBa_R* are the “oldies but goldies” parts by the “Antiquity” team (= the iGEM stuff when iGEM was created). others might be there deposited by various iGEM teams.

Dotplot

Using EMBOSS dotmatcher:

dotmatcher ./data/pOmpR/seq/BBa_R0082.fasta ./data/pOmpR/seq/BBa_R0084.fasta -windowsize 10 -threshold 7 -graph svg
EMBOSS Dotmatcher Dotplot for two promoter sequences of pOmpR
Dotmatcher Dotplots

Multiple Sequence Alignment (ClustalO)

ref. https://bioinformatics.stackexchange.com/a/13416

Install required packages

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ggmsa")
BiocManager::install("Biostrings")
library(Biostrings)
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':

    anyDuplicated, aperm, append, as.data.frame, basename, cbind,
    colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
    get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
    table, tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':

    findMatches
The following objects are masked from 'package:base':

    expand.grid, I, unname
Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'
The following object is masked from 'package:base':

    strsplit
library(ggmsa)
Registered S3 methods overwritten by 'ggalt':
  method                  from   
  grid.draw.absoluteGrob  ggplot2
  grobHeight.absoluteGrob ggplot2
  grobWidth.absoluteGrob  ggplot2
  grobX.absoluteGrob      ggplot2
  grobY.absoluteGrob      ggplot2
Registered S3 methods overwritten by 'treeio':
  method              from    
  MRCA.phylo          tidytree
  MRCA.treedata       tidytree
  Nnode.treedata      tidytree
  Ntip.treedata       tidytree
  ancestor.phylo      tidytree
  ancestor.treedata   tidytree
  child.phylo         tidytree
  child.treedata      tidytree
  full_join.phylo     tidytree
  full_join.treedata  tidytree
  groupClade.phylo    tidytree
  groupClade.treedata tidytree
  groupOTU.phylo      tidytree
  groupOTU.treedata   tidytree
  inner_join.phylo    tidytree
  inner_join.treedata tidytree
  is.rooted.treedata  tidytree
  nodeid.phylo        tidytree
  nodeid.treedata     tidytree
  nodelab.phylo       tidytree
  nodelab.treedata    tidytree
  offspring.phylo     tidytree
  offspring.treedata  tidytree
  parent.phylo        tidytree
  parent.treedata     tidytree
  root.treedata       tidytree
  rootnode.phylo      tidytree
  sibling.phylo       tidytree
ggmsa v1.6.0  Document: http://yulab-smu.top/ggmsa/

If you use ggmsa in published research, please cite:
L Zhou, T Feng, S Xu, F Gao, TT Lam, Q Wang, T Wu, H Huang, L Zhan, L Li, Y Guan, Z Dai*, G Yu* ggmsa: a visual exploration tool for multiple sequence alignment and associated data. Briefings in Bioinformatics. DOI:10.1093/bib/bbac222
library(msa)
dna_sequences_fasta <- ".././data/pOmpR/seq/merged_pOmpR.fasta"
dna_sequences <- readDNAStringSet(dna_sequences_fasta)
ggmsa(dna_sequences, color="Clustal")
Warning in rbind(c("T", "C", "C", "C", "T", "T", "G", "C", "A", "T", "T", :
number of columns of result is not a multiple of vector length (arg 2)

Boshade plot

Boxshade is a C program that allows to plot multiple sequence alignment representations. I installed it from sources.

boxshade -dna -in=./results/pOmpR_antiquity_alignment.aln -out=./media/pOmpR_antiquity_alignment.aln -cons -ruler -par="/Projects/others/boxshade/box_dna.par"

does not work.

Local alignment between regulatory part and composite part

Smith-Waterman local alignment of BBa_K1017301 composite part against BBa_R0082 pOmpR regulatory part, assuming BBa_R0082 sequence is in BBa_K1017301:

water ./data/pOmpR/seq/teams/composites/BBa_K1017301.fasta ./data/pOmpR/seq/BBa_R0082.fasta

References