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.


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:


Reply via email to