[Bioperl-l] off by one problem w/exonerate & search2gff.pl ?

[Charles Hauser]

All,

I am trying to reconcile coordinates generated by exonerate w/ those
using search2gff.pl. 

$ search2gff.pl -i /usr/local/pkg/exonerate/exonerate-0.7.0/s1_100h_500s  -f exonerate -t hit


Below are sample outputs  from exonerate and search2gff.pl.  

			query		target
	cigar line	532->661	58163->58298	
	gff output	533->660	58171->58298


Query appears to be off by 1, whereas target start is off by 8???

Ideas why the target values are off?


Charles





exonerate output:

C4 Alignment display:
  Model: est2genome
  Raw score: 457
  Aligned positions 532->661 of query
  Aligned positions 58163->58298 of target

Query: 832009G03.x1
Target: scaffold_1

   533 : GCCACGTCTCCAGTTTGAGGCCGCAAGCGTCTACCTCATCTCCCGGACATAGCCGGGGTT :   591
	 ||||||| || ||| ||||||||||||||||| ||||||||||||||||||||||||||
 58164 : GCCACGTATCGAGTCTGAGGCCGCAAGCGTCTGCCTCATCTCCCGGACATAGCCGGGGTC : 58222

   592 : GGTTCG--CA-C-GGCACGGCCCGCCATA---TGTCCAGCCACGTCCCGCTGGCAAGGAC :   644
	 ||||||  || | ||||||||||||| ||   |||||||||||||||||||  |||| ||
 58223 : GGTTCGTACAGCAGGCACGGCCCGCCGTACTGTGTCCAGCCACGTCCCGCTTCCAAGCAC : 58282

   645 : AAGCCCAGCCAGGCAA :   661
	 |||| ||| || ||||
 58283 : AAGCACAG-CAAGCAA : 58298

cigar: 832009G03.x1 532 661 + scaffold_1 58163 58298 + 457 M 66 D 2 M 2 D 1 M 1 D 1 M 16 D 3 M 36 I 1 M 7


search2gff.pl output:

scaffold_1	EXONERATE	similarity	58171   58298   457	+	0	Target "Sequence:832009G03.x1"  533 660