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

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

next-gen sequence genome
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updated by Antonio R. Franco Antonio R. Franco • written by biomoon • biomoon

3 answers

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).

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written by dlyons • dlyons

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

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written by biomoon • biomoon

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.

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written by GenoMax GenoMax

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

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written by biomoon • biomoon

Look for a gff or gft file of your genome.

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

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written by Antonio R. Franco Antonio R. Franco

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.

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written by biomoon • biomoon

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

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written by Antonio R. Franco Antonio R. Franco

@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

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written by GenoMax GenoMax

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