CoroAnnoter

A semi-automatic coronavirus genome annotation tool

Pipline

Data Preparation

Coronavirus genome

blastdb

Soft Preparation

R, MEME, blast, ORFfinder

Annotation

ORF finder

   ORFfinder -in ${samplename}.fasta -g 1 -s 0 -ml 60 -out ${samplename}.ORF -outfmt 0

BLAST

   blastp -query ${samplename}.ORF -db ${blastdb} -evalue 1e-2 -max_target_seqs 3 -out ${samplename}.blast_out.xls -outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore slen stitle qcov"

Manually remove redundant blast results

####The blastdir contain genome and BLAST results：SARS_CoV-2.fasta, SARS_CoV-2.blast.*.xls

   source("./R/merge_blast.R")

   merge_blast("./inst/extdata")

####The SARS_CoV-2.xls file were created.

####Manually process blast results to remove redundant ID.

Get TRS

   source("./R/getTRS.R")

   GetTRS(blastfile = "./inst/extdata/Manual-SARS_CoV-2.xls", 
   genomefile = "./inst/extdata/SARS_CoV-2.fasta")

MEME prediction motif

   system("sh ./R/meme.sh ./inst/extdata/TRS")

Draw protein

   source("./R/pairwise_alignment.R")

   pairwise_alignment(core_seq = "ACGAAC",
               genomefile = "./inst/extdata/TRS/Manual-SARS_CoV-2.TRS.fasta")

   source("./R/get_motif_location.R")

   get_motif_location(genomefile = "./inst/extdata/SARS_CoV-2.fasta","ACGAAC")

   source("./R/plot_protein_single.R")

   plot_protein_single(anno_R = "./inst/extdata/Manual-SARS_CoV-2_anno.csv",
                TRSlocation = "./inst/extdata/TRS/SARS_CoV-2.TRS")

Download

The development version can be installed through github:

   devtools::install_github(repo="wuaipinglab/CoroAnnoter")

   library(CoroAnnoter)