[Bioperl-l] search2gff

Neil Saunders neil.saunders at unsw.edu.au
Fri Jul 2 01:45:41 EDT 2004

I have a couple of queries regarding the search2gff script.

1) I'm using the latest CVS (1.8) which states "search2gff does the 
right thing now - now strand is done right properly".  Am I right in 
thinking that now target start is always less than target end?

2) Should search2gff work with any BLAST flavour?

I ask because I'm running it on tblastx files.  Without the -m switch 
it seems to run fine, but if I add -m, I get thrown exceptions looking 
like e.g. :

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Undefined sub-sequence (2827710,2827711). Valid range = 2827710 - 

The undefined subsequence start/ends always differ by 1.

 School of Biotechnology and Biomolecular Sciences,
 The University of New South Wales,
 Sydney 2052,


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