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

[Jason Stajich]

I thought I had fixed this per bug reports though - not sure if fix was
made on the branch though.


On Wed, 9 Jul 2003, Charles Hauser wrote:

> 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
>
>
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu