[Bioperl-l] Trace coordinates from scf files

SRMD, Col - Underwood, Anthony Anthony.Underwood at hpa.org.uk
Tue Mar 2 08:30:06 EST 2004

Hi Bioperlers and Chad

As a follow up to my last message on the bioperl-mailing list:

I can see that the follwing methods do the following
$seq->length() returns the length in bases of the sequence held within the
scf file
$seq->trace_length() this returns the number of points for the trace data
print $seq->baseat("64") returns the base at position 64 in the sequence
print $seq->qualat("64") returns the quality at position 64 in the sequence
$seq->peak_indices() returns the peaks heights at each of the sequence

however I find the $seq->trace("G") method a bit mysterious
the array returned has $seq->trace_length() elements and the values are
cumulative ( I think I may be dealing with a version 2 scf file). I
understand that the trace values should be calculated based on delta values.

something like $current_delta=$current_value-$previous_value

This doesn't quite work. Please could anybody enlighten me on how the trace
values can be convrted into points that plotted as sequential "Y" values
would represent points on  a curve that resemble the traces when viewed in a
an application such as Chromas.

Many thanks,


Dr Anthony Underwood
Bioinformatics Group
Genomics, Proteomic and Bioinformatics Unit
Central Public Health Laboratory
Health Protection Agency
61 Colindale Avenue
t:    0208 2004400 ext. 3618
f:    0208 3583138
e: anthony.underwood at hpa.org.uk

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