Hi all, I'm about to start working on a general tool for extracting sequences (from FASTA etc) based on a tabular file describing desired regions (this could be a BED or GFF3 file), giving a new sequence file with one entry for each region in the tabular file. Essentially I want as input columns describing:
* FASTA sequence ID * Start * End * Strand (optional) * Region ID for this sequence in the output file (optional) In the case of a GFF3 input, those would be columns 1, 4, 5, 7 (with the ID being hidden inside column 9). But this isn't really driven by GFF3 where you'd probably not want to treat each line separately anyway (compound features). I'm thinking of very general examples like extracting general search matches (BLAST, HMMER, motifs, etc), but specifically things like cleaving proteins to remove a predicted signal peptide. This could even be used for trimming of sequencing reads (for small datasets, e.g. capillary reads). Is there anything like this in Galaxy already? If so I can't find it ;) I've also skimmed the tool shed. Regards, Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
