convert tRNA coordinates Result to Fasta format I believe many of the experts here have gone through this issue,

I have run tRNAscan-SE on my genome to predict all the tRNAs, and have successfully gotten all the tRNA coordinates like start, end and type all  arranged in a table.

My question is how can I convert this result to fasta format as long I have all the details about the tRNA ready?

Is there any tool that I can use to get the fasta sequences of the regions described in my table from the original genome?





Sequence                tRNA    Bounds  tRNA    Anti    Intron Bounds   Inf       
Name            tRNA #  Begin   End     Type    Codon   Begin   End     Score   Note
--------        ------  -----   ------  ----    -----   -----   ----    ------  ------
NW_011590950.1  1       36704   36632   Ala     AGC     0       0       40.8    pseudo
You can select “Output BED format” on the tRNAscan-SE server:



Given the output BED format and your input reference in FASTA format, you can easily generate a FASTA file of tRNA sequences via bedtools getfasta:

bedtools getfasta -name -s -fo ‹output.fasta› -fi ‹reference.fasta› -bed ‹tRNAscan-SE-output.bed›