[Bioperl-l] Fasty frameshift-characters

[TAPO (Thomas Agersten Poulsen)]

Dear BioPerl list,

	I am using Bio::SearchIO(-format=>"fasta") to parse the output from FASTY, but I do not get the frameshift-characters ('/' and '\') in the  sequences returned by next_result->next_hit->next_hsp->get_aln->each_seq->seq(). This is apparently independent of what 'missing_char' is set to.
	Please, can anybody help me recover the frameshift information?

Sincerely
Thomas Poulsen

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Thomas A Poulsen       Research Scientist, PhD, MSc
Novozymes A/S           Protein Design / Bioinformatics
Brudelysvej 26, 1US.24  Phone: +45 44 42 27 23
DK-2880 Bagsværd.       Fax:   +45 44 98 02 46