KEGG Sequence Downloader : retrieve gene sequences in Fasta format from KEGG database
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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
How to download only viridiplantae miRNA from miRBase HERE
Script
| Script name | Download |
|---|---|
| KEGG_sequence_downloader.sh |  |
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