How to retrieve all the intron sequences and information (e.g. location) if I have a genome. Thanks in advance!
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).
Thanks. I have gtf file and a genome sequence. Bedtools can do that, right?
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.
Thank you. Good idea for a genome available in website. What I want is to get intron sequence from a new genome.
Look for a gff or gft file of your genome.
If no present, you can try some annotation using programs like genemark, August, et
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.
Can you be more precise indicating what exactly do you want to get?
@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