seqcombo for sequence recombination

Sequence difference plot

Here we use the data published in Potato Research(Chang et al. 2015) as an example.

fas <- list.files(system.file("examples","GVariation", package="seqcombo"),
                  pattern="fas", full.names=TRUE)
fas

## [1] "/tmp/Rtmpnghtdv/Rinst1299534c3212/seqcombo/examples/GVariation/A.Mont.fas"  
## [2] "/tmp/Rtmpnghtdv/Rinst1299534c3212/seqcombo/examples/GVariation/B.Oz.fas"    
## [3] "/tmp/Rtmpnghtdv/Rinst1299534c3212/seqcombo/examples/GVariation/C.Wilga5.fas"

The input fasta file should contains two aligned sequences. User need to specify which sequence (1 or 2, 1 by default) as reference. The seqdiff function will parse the fasta file and calculate the nucleotide differences by comparing the non-reference one to reference.

x1 <- seqdiff(fas[1], reference=1)
x1

## sequence differences of Mont and CF_YL21 
## 1181 sites differ:
##   A   C   G   T 
## 286 315 301 279

We can visualize the differences by plot method:

plot(x1)

We can parse several files and visualize them simultaneously.

x <- lapply(fas, seqdiff)
plts <- lapply(x, plot)
plot_grid(plotlist=plts, ncol=1, labels=LETTERS[1:3])

Sequence similarity plot

fas <- system.file("examples/GVariation/sample_alignment.fa", package="seqcombo")
simplot(fas, 'CF_YL21')

Session info

Here is the output of sessionInfo() on the system on which this document was compiled:

## R version 4.0.3 (2020-10-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.5 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.12-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.12-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] igraph_1.2.6    ggplot2_3.3.2   emojifont_0.5.3 tibble_3.0.4   
## [5] seqcombo_1.12.0
## 
## loaded via a namespace (and not attached):
##  [1] BiocManager_1.30.10 compiler_4.0.3      pillar_1.4.6       
##  [4] XVector_0.30.0      sysfonts_0.8.1      prettydoc_0.4.0    
##  [7] tools_4.0.3         zlibbioc_1.36.0     digest_0.6.27      
## [10] evaluate_0.14       lifecycle_0.2.0     gtable_0.3.0       
## [13] pkgconfig_2.0.3     rlang_0.4.8         rvcheck_0.1.8      
## [16] yaml_2.2.1          parallel_4.0.3      xfun_0.18          
## [19] proto_1.0.0         withr_2.3.0         showtextdb_3.0     
## [22] stringr_1.4.0       dplyr_1.0.2         knitr_1.30         
## [25] Biostrings_2.58.0   generics_0.0.2      S4Vectors_0.28.0   
## [28] vctrs_0.3.4         IRanges_2.24.0      stats4_4.0.3       
## [31] grid_4.0.3          cowplot_1.1.0       tidyselect_1.1.0   
## [34] glue_1.4.2          R6_2.4.1            rmarkdown_2.5      
## [37] farver_2.0.3        purrr_0.3.4         magrittr_1.5       
## [40] scales_1.1.1        htmltools_0.5.0     ellipsis_0.3.1     
## [43] BiocGenerics_0.36.0 showtext_0.9        colorspace_1.4-1   
## [46] labeling_0.4.2      stringi_1.5.3       munsell_0.5.0      
## [49] crayon_1.3.4

References

Chang, Fei, Fangluan Gao, Jianguo Shen, Wenchao Zou, Shuang Zhao, and Jiasui Zhan. 2015. “Complete Genome Analysis of a PVYN-Wi Recombinant Isolate from Solanum Tuberosum in China.” Potato Research 58 (4):377–89. https://doi.org/10.1007/s11540-015-9307-3.