Wednesday 23 January 2013

Inferring transcript sequences from a gff file

Have you ever been given a gff file of gene predictions, but wanted to infer the transcript sequences (ie. the DNA sequences that would be translated into protein sequences) for the genes? I've written a perl script get_spliced_transcripts_from_gff.pl that does this, based on an input gff file of gene predictions, and an input fasta file of chromosome/scaffold sequences.

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