How to retrieve all the intron sequences and information (e.g. location) if I have a genome.

Question

[biomoon]

How to retrieve all the intron sequences and information (e.g. location) if I have a genome. Thanks in advance!

Answer 1

[dlyons]

combine your exon and UTR files, then do a "bedtools intersect -v" against the gene file. everything remaining is intron (or at least this would be a good first guess).

[biomoon]

Thanks. I have gtf file and a genome sequence. Bedtools can do that, right?

Answer 2

[GenoMax]

If it is one of the genomes available at UCSC/Ensembl you could use Table browser/BioMart (click on BioMart is top navigation bar) respectively to get that information.

[biomoon]

Thank you. Good idea for a genome available in website. What I want is to get intron sequence from a new genome.

Answer 3

[Antonio R. Franco]

Look for a gff or gft file of your genome.

If no present, you can try some annotation using programs like genemark, August, et

[biomoon]

Thanks. I have got a gtf file using augustus. Can you tell me how to put all intron sequences to a single file? Thank you.

[Antonio R. Franco]

Can you be more precise indicating what exactly do you want to get?

[GenoMax]

@biomoon: If you have a GTF file then can you see annotations labelled as "introns"? You can use the answer in this thread to get the sequence: convert bed file to fasta file