SCF (Alfx, Licor, CEQ2000 and Phred

Phillip San Miguel pmiguel at purdue.edu
Mon May 15 11:41:15 EST 2000

    What is the general consensus on Phred's ability to call bases in SCF files
exported from various sequencers?
    Licor and CEQ2000 softwares have the capability of creating phd files (which have
both the bases and quality scores for each base in a single file). One would think
that a sequencer manufacturer would be able to write software that did a better job
of basecalling and quality assignment--for their own chromatograms--than phred, which
was trained on ABI 373/377 chromat files.
    Finally, does anyone know of a utility that would export an SCF file from the
*processed* chromatogram of an Alf express. I run Alfwin1.1--which will export SCF
format files, but I suspect they are unprocessed--because phred does a marginal/bad
job of calling bases from these SCF files. The Alfx software does a great job, but
doesn't assign quality scores--making it nearly useless for assembling with ABI data.
Any input on this topic would be useful.

Phillip San Miguel
Purdue University Genomics Core Facility

PS. Am I alone in finding the 3 "Message not deliverable:Unknown cc:Mail recipients"
, 1 "Email Address Change -- Please Note" and recently, 1 "Edwin F Roovers/EUR/PEC is
out of the office." emails from PE Biosystems in response to every message one posts
to this group irritating? I wouldn't mind if it were an isolated occurance--but it
has been going on for *years*.  I actually think twice about posting to this group
because I know I'll be getting these responses from PE Biosystem's deranged mailer
    I've actually tried to email a sysadmin at PE Biosystems about this--but have
never gotten a response...


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