Gallery - Example 6

Below is the R code to reproduce the example:

Hide output

library(DECIPHER)
> 
> genomes <- c(`Y. pestis antiqua`="Yersinia_pestis_Antiqua_uid58607/NC_008150",
+    `Y. pestis CO92`="Yersinia_pestis_CO92_uid57621/NC_003143",
+    `Y. pestis KIM10`="Yersinia_pestis_KIM_10_uid57875/NC_004088",
+    `Y. pestis Microtus`="Yersinia_pestis_biovar_Microtus_91001_uid58037/NC_005810",
+    `Y. pestis Nepal`="Yersinia_pestis_Nepal516_uid58609/NC_008149",
+    `Y. enterocolitica palearctica`="Yersinia_enterocolitica_palearctica_105_5R_r__uid63663/NC_015224",
+    `Y. pestis Pestoides`="Yersinia_pestis_Pestoides_F_uid58619/NC_009381",
+    `Y. pseudotuberculosis IP31758`="Yersinia_pseudotuberculosis_IP_31758_uid58487/NC_009708")
> 
> dbConn <- dbConnect(SQLite(), ":memory:")
> path <- "ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Bacteria/"
> for (i in seq_along(genomes)) {
+    Seqs2DB(paste(path,
+          genomes[i],
+          ".fna",
+          sep=""),
+       "FASTA",
+       dbConn,
+       names(genomes)[i],
+       verbose=FALSE)
+ }
> 
> # find syntenic blocks
> synteny <- FindSynteny(dbConn)
  |============================================| 100%


Time difference of 30.16 secs


> 
> # display a dot plot
> labels <- sapply(lapply(strsplit(rownames(synteny), " "),
+          abbreviate,
+          minlength = 9),
+    paste,
+    collapse="\n")
> pairs(synteny, labels=labels)
> 
> # display a bar plot
> plot(synteny)
> 
> # align syntenic blocks
> DNA <- AlignSynteny(synteny, dbConn)
  |============================================| 100%


Time difference of 578.24 secs


> 
> dbDisconnect(dbConn)
[1] TRUE