Dear all,
I recently Beta tested the Paracel base calling software. It worked on the
raw data not the called data. It was very good. It gave me about a 20
percent increase in bases called and cleared up some of the ambiguities that
the ABI software called. It also gave a confidence call for each base as
well. It may be out I don't know but you can check if its out on thier
website. www.paracel.com
Sincerely,
Douglas Spicer
Scientist
Prolinx, Inc.
22322 20th Avenue SE
Bothell, WA 98021
T 425-487-3401 ext.112
F 425-487-9578
-----Original Message-----
From: James VanEe [mailto:jiv2@cornell.edu]
Sent: Monday, April 09, 2001 6:42 AM
To: Recipients of ABRF List
Subject: Re: DNASEQ: Skewed nucleotide composition
I'd certainly be interested in the results. I think success might
depend on whether this adjustment (normalization?) for assumed
composition happens in the same stage as mobility adjustments and
whatnot that take the raw florescence data and change them to the
peaks we know and love. I believe phred is starting from the
processed peaks given to it by the abi (or other) software - the
damage might be done at that point. There are alternatives for the
intitial processing steps, but I can't list them off the top of my
head with any authority. the phred papers (genome research
8:175-185) mention "plan" (B. Ewing and P. Green, in prep.) but I
couldn't find a published paper. I know I've come across other "lane
processors": BASS
(http://www.genome.wi.mit.edu/ftp/distribution/software/Bass/doc/BASS.html)
or maybe these are something to build on (but I notice they are not
currently available:
http://ravel.zoology.wisc.edu/sgaap/Bioinformatics.htm
>Hi Bob,
>
>Have you tried an different software program that might have a different
>basecalling algorithm? One possibility is to analyze the results with
>phred. If you do not have phred readily available, just send me some
>chromatogram files and I would be happy to give it a try.
>
>ABI should take note that many labs would love to use flourescent
>sequencing to detect methylayed C's. Nice trick regarding the hidden menu
>for 377s. Did you find it by randomly banging the keyboard in fustration?
>
>- George
-------------------------------------------------------------------
James VanEe Phone: (607) 254-4862
BioResource Center
Computing Facilty
170/171 Biotech Bldg Fax: (607) 254-4847
Cornell University
Ithaca, NY 14853 www: http://brcweb.bio.cornell.edu
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