I wanted to download the gene sequence of tobacco from NCBI. Since NCBI also contains the isoform and some other unwanted genes, therefore I choose to get it from KEGG. Although KEGGREST is a wonderful R package to retrieve the data from KEGG, but it limits the retrieval. The following bash script can help to download the thousands of sequences in a single go without any limitation. Although this is a crude solution and there must be an efficient way to do it but it worked for me. Basically, this bash script works in three steps:

• Split IDs in a given chunk 


• Download fasta sequences as HTML file 


•  Clean HTML file and save the result
  

Uses

bash KEGG_sequence_downloader.sh query_file number_of_sequence

Script

Script name	Download
KEGG_sequence_downloader.sh