Introns identification in genome reference file

Question

[mohammadborooshaki]

Hi everybody

I have a reduced genome fasta files which has only one chromosome(not the whole genome). this is a refrence genome(not transcriptome). how can I identify the introns and exons from a fasta file? what I have to do for my project is to remove the introns but I do not know how to distinguish them. Is there a way to find the introns from a fasta file? Thanks for any help

Answer 1

[GouthamAtla]

What genome are you working with ? Is this home work ? If its home work, try to get the GTF file for the genome and then fetch transcriptome from gffread which excludes introns. If you are skilled at programming, you could also write a script to extract parts of fasta sequence that overlap exon coordinates from GTF.

If you dont have a reference GTF, you may need to depend on some gene prediction tools.

[mohammadborooshaki]

Yeah it is kinda homework. it is a Drosophila melanogaster genome.