ABI Prism® 3700 DNA Analyzer Beta Basecaller for data
generated with POP-5™Polymer
Basecaller v1.1B2 Release Notes
Release Notes Rev D
June 01, 2000
3700 DNA Analyzer System/Sequencing Analysis Software™
PE Biosystems
INTRODUCTION
A beta basecaller package has been developed to address basecalling issues for data generated on ABI
Prism® 3700 DNA Analyzer systems with BigDye™ terminator and POP-5™ Polymer.
Beta software is software still under development and requires several cycles of testing and algorithm
optimization before it becomes a final software product. This basecaller has not been through all these
cycles. Our initial testing has shown significant basecalling improvements with most but not all templates.
The beta basecaller software will not provide solutions to all basecalling problems.
This beta basecaller package has been developed to improve mobility shift problems primarily seen in the
first 100 bases in data generated with BigDye™ terminator and POP-5™ Polymer on the 3700 systems with
Data Collection version 1.1 and Sequencing Analysis Software™ version 3.6.
Document Contents:
1. Basecaller overview
2. Contents of beta basecaller package
3. Changes in beta basecaller package
4. Compatibility and when to use beta basecaller package
5. Installation instructions for beta basecaller package.
1. Basecaller overview:
---------------------------------The Basecaller is the application that analyzes raw data from the ABI Prism® 3700 DNA Analyzer and
generates basecalls. The Basecaller is a dynamic linked library (dll) that is executed either from Sequencing
Analysis Software™ or AutoAnalyzer. There is no user interface for the basecaller application. The
Basecaller is used in conjunction with a bcp file and a mobility (mob) file. Your existing ABI Prism® 3700
DNA Analyzer system should have a single Basecaller.dll file, several Basecaller.bcp files and several
mobility files.
Sequencing
Analysis v3.6
Raw
Data
Or
Basecaller.dll
Basecaller.bcp
Mobility file
Analyzed
Data
Auto
Analyzer
The Basecaller.dll, using the algorithm parameters in the Basecaller.bcp file and the mobility shifts in the
mobility file, processes raw data to produce basecalls.
The beta Basecaller package v1.1B2 contains a beta dll file, a beta bcp file and a beta mobility (mob) file
and a saz file. The first three files should be used together to obtain improved results on data generated on
ABI Prism® 3700 DNA Analyzer systems with BigDye™ terminator and POP-5™ Polymer.
2. Contents of the beta basecaller package:
------------------------------------------------------------The beta Basecaller v 1.1B2 package contains 4 files: Basecaller.dll, Basecaller-POP5opt.bcp,
DT3700POP5{BD}v3.mob and BC-POP5opt_FacOffSeqOff.saz.
The Basecaller.dll (beta version) file is designed to replace your existing Basecaller.dll file. The BasecallerPOP5opt.bcp and DT3700POP5{BD}v3.mob files are designed to be additions to your current
Basecaller.bcp files and mobility files. The BC-POP5opt_FacOffSeqOff.saz file is designed to be an
addition to your current saz files.
3. Changes in beta basecaller package:
--------------------------------------------------Changes in the Basecaller.dll version 1.1B2:
The beta basecaller file is called Basecaller.dll version 1.1B2. This version of the basecaller has been
optimized to correct mobility shift problems seen with data generated on ABI Prism® 3700 DNA Analyzer
systems with BigDye™ terminator and POP-5™ Polymer. It contains an adaptive spacing algorithm that
optimizes the spacing correction of each base and produces more evenly spaced analyzed data, particularly
in the first 100 bases of a sequence.
Note: Only a single Basecaller.dll file should exist in the Perkin-Elmer\Abi\Shared\Bin directory. Please be
sure to archive the existing Basecaller.dll file and replace it with the beta Basecaller.dll file. Attention is
required because both the existing and the beta Basecaller.dll have identical names. To verify that your
system is using the correct version, open the Annotation view of the sample file after analysis and check for
v1.1B2 in the version number field.
Changes in the BCP file:
The beta bcp file is named Basecaller-POP5opt.bcp. This bcp file, when used with the beta Basecaller.dll,
invokes the adaptive spacing algorithm. Use this bcp file to analyze data generated on ABI Prism® 3700
DNA Analyzer systems with BigDye™ terminator and POP-5™ Polymer.
You can still use existing Basecaller-Pop5LR.bcp file with this beta Basecaller.dll if desired, but only the beta
Basecaller-POP5opt.bcp file will enable the adaptive spacing algorithm.
Changes in the mobility file:
The beta mobility file is named DT3700POP5{BD}v3.mob. This mobility file has been tuned to improved the
mobility correction in data generated on ABI Prism® 3700 DNA Analyzer systems with BigDye™ terminator
and POP-5™ Polymer.
Changes in the saz file:
In the sample sheet of Data Collection Software, select this saz file to have the AutoAnalyzer invoke the
Basecaller-POP5opt.bcp file to analyze data generated with POP-5™ Polymer.
4. Compatibility and when to use the beta Basecaller package:
--------------------------------------------------------To call bases for data generated with BigDye™ terminator and POP-5™ Polymer, use these files: (evaluate analyzed data for
improved results)
Chemistry Type
DLL file
BCP file
MOBILITY file
POP-5™ Polymer
Basecaller.dll v.1.1B2
Basecaller-POP5opt.bcp
DT3700POP5{BD}v3.mob
(beta)
(beta)
(beta)
Big Dye™ terminator
To call bases for data generated with POP-5™ Polymer and Big Dye™ primer or dRhodamine, use these files: (Same results as
when analyzed with Basecaller.dll version 1.1)
Chemistry Type
DLL file
BCP file
MOBILITY file
DP3700POP5{BD-21M13}v1.mob or
POP-5™ Polymer
Basecaller.dll v.1.1B2
Basecaller-POP5LR.bcp
(beta)
Big Dye™ Primer
DP3700POP5{BD-M13Rev}v1.mob
POP-5™ Polymer
Basecaller.dll v.1.1B2
Basecaller-POP5LR.bcp
DT3700POP5{dRhod}v1.mob
(beta)
dRhodamine
To call bases for data generated with POP-6™ Polymer and Big Dye™ primer or Big Dye™ terminator or dRhodamine, use
these files: (same results as when analyzed with basecaller dll version 1.1)
Chemistry Type
DLL file
BCP file
MOBILITY file
DP3700POP6{BD-21M13}v3.mob or
POP-6™ Polymer
Basecaller.dll v.1.1B2
Basecaller-Pop6.bcp
(beta)
Big Dye™ primer
DP3700POP6{BD-M13Rev}v2.mob
POP-6™ Polymer
Basecaller.dll v.1.1B2
Basecaller-Pop6.bcp
DT3700POP6{BD-}v5.mob
(beta)
Big Dye™ terminator
POP-6™ Polymer
Basecaller.dll v.1.1B2
Basecaller-Pop6.bcp
DT3700POP6{dRhod}v3.mob
(beta)
dRhodamine
5. Installation instructions for beta basecaller package:
----------------------------------------------------------------------------------------------Step A: Quit Sequencing Analysis Software™
Step B: Archive your existing Basecaller.dll file for future usage. Create a new archive folder and move to
this new folder the existing Basecaller.dll file located in Perkin-Elmer\Abi\Shared\Bin directory.
Step C: Downloading the beta Basecaller v1.1B2 package which contains 4 files: Basecaller.dll, BasecallerPOP5opt.bcp, DT3700POP5{BD}v3.mob and BC-POP5opt_FacOffSeqOff.saz.
Step D: Place the following files into the corresponding folders:
1. Basecaller.dll
Place into folder: Perkin-Elmer\Abi\Shared\Bin.
2. Basecaller-POP5opt.bcp
Place into folder: PerkinElmer\Abi\Shared\Analysis\Basecaller\Params
3. DT3700POP5{BD}v3.mob
Place into folder: Perkin-Elmer\Abi\Shared\Analysis\Basecaller\Mobility
4. BC-POP5opt_FacOffSeqOff.saz
Place into folder: Perkin-Elmer\Abi\Shared\Analysis\Basecaller\ Params
Step E: Launch Sequencing Analysis Software™ and analyze your data.
Step F: When creating a new sample sheet in Data Collection Software, select the saz file
BC-POP5opt_FacOffSeqOff.saz. The AutoAnalyzer will invoke the Basecaller-POP5opt.bcp file to analyze
the corresponding sample files.
Step G: To verify that your system is using the beta Basecaller.dll, open the Annotation view of the sample
file after analysis and check for “v1.1B2” in the basecaller version number field.
ABI Prism is a registered trademark and Sequencing Analysis Software, Big Dye, POP-5 and POP-6 are
trademarks of PE Corporation or its subsidiaries in the US and certain other countries.