How to retrieve/extract specific intergenic regions?

Question

[geizetomazetto]

Hi Folks,

A database was constructed for a target protein sequences, including protein_ID, start codon, stop codon, BioSample, and Assembly Accession. It means, the data has a lot of “XX” protein sequences from different bacterial genomes.

Now, I would like to use this information to retrieve/extract only the sequences after stop codon. So far, I only found to retrieve/extract all intergenic region. I need a specific region. I also tried to adapt the script from https://www.ncbi.nlm.nih.gov/books/NBK179288/ -- Given a shell script named "upstream.sh".

Without successful. Anyone could give me some tips?

[h.mon]

For a bacterial genome with no introns, and if you have the gff / gtf genome annotation file, bedtools subtract or bedops --difference would do the trick.

[geizetomazetto]

Hi ..

I appreciate your hits. However, only for E. coli there are 8,000 sequences. To download gff and extract them, I do not know if it would not be much easy.

[vkkodali_ncbi]

Can you provide an example of your input table? Specifically, what are the start and stop coordinates you have? As long as you can get to a BED-like file with chromosome, start position, end position and strand information you can always download the entire genomes in FASTA format first and use bedtools getfasta to extract downstream sequences.