BaseFinder 6
What is BaseFinder?
It's a tool for processing trace data for
DNA sequencing, or for analysis of SHAPE data. It was
written primarily by Morgan Giddings and Jessica Severin at
the University of Wisconsin-Madison, in Lloyd Smith's lab.
The program was started in 1991 by Morgan, and continued
refinement through 1997. More recently, it has been
maintained by Morgan Giddings at the University of North
Carolina at Chapel Hill. giddings@unc.edu.
How to Install?
Prior to installation, it is best to manually delete the
previously installed BaseFinder. Next, Drag and Drop the
BaseFinder.app file into the Applications folder. If you
have a release prior to 6.1.11, please remove all files
from the directory /Library/BaseFinder/Resources.
Otherwise, you'll see some error messages when starting
BaseFinder. Enjoy!
How to Build?
Open the file BaseFinder/BaseFinder.xcodeproj in Xcode and
build. Intel Mac? Not to worry, BaseFinder is set up to
build as a universal binary and yet supports OSx 10.3.9.
Have fun!
And....
Tools, Align and Integrate and Decay Correction, are not
included at this time. These tools will be released at a
later date.
Other contributors:
Mike Koehrsen
Suzy Vasa
Nicolas Guex
HISTORY
BaseFinder Release Notes
Version 6.2.3
-ddNTP nucleotides can now be deleted by Align and
integrate
-More strict on what is considered an outlier for Signal
Decay tool--1.5IQR instead of 3*IQR
Version 6.2.2
-Mobility Shift: Polynomial can now shift all 8 channels.
-New option for enable/disable hash line marking of base
locations
-New low peak cutoff option added to Tool TRFLP
-Help book page for TRFLP tool
-Fix bug in Align and Integrate: tool wasn't executing at
Append.
-Fix bug in Signal Decay Correction tool. Can't begin
interative procedure with coefficients initialized to 0.
Version 6.2.1
-Selected channel Manual Deletion now available, only
possible with the "leave a space" option checked.
Otherwise, the range is deleted from all channels.
-BFNewTool framework was not used and so was removed from
the project.
-Support for fitting first and last peaks in Align &
Integrate is now available.
-Fix Replace problem if interactive tool is the first tool
-Fix error with parameter reset issues for interactive
tools
-can drag and drop to open files in BaseFinder
-fixed memory leak with lots of files open
-fixed error when multiple files are selected and command-S
is entered
-improvements to tool T-RFLP, annotation of peaks, primer
peak clean up
-improvements to the Help Book
Version 6.2.0:
-Align and Integrate is now classified as an interactive
tool, allowing the REPLACE option to reuse the same cache.
-New tool for correcting signal decay is introduced--Signal
Decay Correction
-Fixed crash for undefined colors in channels 5-8.
-Loaded files panel won't disappear anymore
-Sequence labels for Align and Integrate tool were not
displayed in some situations
-More work done on background processing of Align and
Integrate fitting. Can fit more then one trace
-Sequence produced from Align and integrate reflects
correct order of sequence when markers are displayed, i.e.,
reversed.
Version 6.1.19:
-BigEndian conversion to native format was using
NSSwapBigShortToHost which used unsigned 16 bit integers as
input. ABI
raw data is stored as signed 16 bit integers. Negative
numbers were converted to huge positive numbers.
Changed to EndianS16_BtoN.
-.dat and .seqd save as version were flipped
Version 6.1.18:
-fix crash with standard marker implementation
-introduction of new Levenberg-Marquardt curve fitting
algorithm
-introduction of Cubic spline algorithm for point
interpolation
-Help Book now accessible through the BaseFinder Help menu
-Fix problem with losing input data in Align &
Integrate
-Filter-Convolution should show only channels that were
selected for filtering
-Fix crash in RNAfit when a peak area is 0
-Fine tuned algorithm for identifying peaks to add
Version 6.1.17:
-fix crash in AsciiArchiver again
-framework for Align and Integrate background threads
implemented--not enabled.
-new tool for T-RFLP
Version 6.1.16:
-fix crash in AsciiArchiver--crash when loading certain
files
-problem with empty base list when reading FSA files.
Version 6.1.15:
-fix error with how buttons enabled for align and integrate
-change from CAGT to 1234 in Matrix tool and Mobility shift
tools
-rnafit v0.82 now integrated
-fix problem with adding peaks.
-added new save option .shape
-peak squares somewhat transparent
-user selected y scale carries over to printing
-Under Display Options, Data Marker, user can select if the
sequence postitions or trace data position will be shown.
Version 6.1.14:
-integrated rnafit v0.81
-introduction of UI improvements and enhancements
-multiple files can now be loaded and analyzed using Align
and Integrate tool without data conflicts between files
-fixed clipping of peak indications. However there are
still problems with magnifications below 75%
-can now add ddNTP peaks
-can add reagent, background and ddNTP peaks by single
click on main viewing window--no longer need to select the
table column.
-smoothing option added in the setup panel
-smart channel selection added in the setup panel
-fixed crash in mobility shift tools
-fixed crash when reading extra long Sequence files
-when channels are reordered by the Align and Integrate
tool, the color is reordered too.
-changed ordering of channels read from ABI files
-fixed errors in handling more then 4 channels in the Align
and Integrate tool
Version 6.1.13:
-Modifications to build settings to support intel Mac and
universal binaries--10.4 on intel mac and 10.3 on power pc
-fix crash when printing
-For the tool Align and Integrate, smoothing is on by
default
Version 6.1.12:
-restructure of BaseFinder to build from one project with
embedded frameworks
-support added for reading AB1 and FSA files
Version 6.1.11sm:
-Same as version 6.1.11 but with RNAfit smoothing enabled.
Version 6.1.11:
-Integration of RNAfit version 0.8, further improvements to
peak width detection and peak placement
Version 6.1.10:
-Integration of RNAfit version 0.71, improvements in peak
finding and curve fitting
-RNAfit v 0.71 introduced a smoothing function to improve
peak finding. It is turned off in this release in order to
enable further experimentation with Deconvolution Tool.
-Fix error during copy phase during build of bundle
Version 6.1.9:
-Integration of RNAfit version 0.6
Version 6.1.8:
-fix bug with reordering of trace channels by Align Tool
-add support in Align Tool to remove a ddNTP channel from
analysis by the tool
Version 6.1.7:
-Fix lock up bug when transitioning from Init to Modify in
the Align Tool
-Added to Align Tool the ability to save the fitted data
file and the integrated data file
Version 6.1.6:
-Modification to draw ladder utilities. Drawing of
gaussians support for the tool Align and Integrate
-Align and Integrate tool will reorder channels based on
user settings of location of +reagent, -reagent, etc.
Version 6.1.5:
-New tool Align and Integrate which is the integration of
RNAFit into BaseFinder
Version 6.1.4:
-Fixed problem with the Mobility tools. Mobility Polynomial
and Mobility Nonlinear could read eachothers files which
caused BaseFinder to crash since the class was incorrect
for the tool.
-Can now open and save .txt files
-BaseFinder supports opening a Beckman .txt file
Version 6.1.3:
-Added new Scale Factor tool for scaling individual
channels
-Fixed an issue with the Manual Deletion Tool. It wasn't
0ing the channels for the leave space option.
-Various changes to support the new Xcode 2.1 version.
Version 6.1.2:
- Fixed scale to go from 0 to 50x, rather than 100x.
- Fixed problem where when sliding traces (e.g. in mobility
tools) the scale isn't correctly set
- Fixed problem where repeated use of mobility tools lost
track of views...
Version 6.1.1:
- Fixed bug with overlapping control of magnification
- Fixed reading of ESD files to correctly place channels
Version 6.1:
- Save now accessed by cmd-s
- Save Current Lane As... was implemented to save an
individual lane
- ESD format can now be opened
- A new scaling control has been added to perform live
re-scaling of the vertical axis. The reset button sets the
scale back to 1.0.
- Various internal bug fixing
Known bugs/issues
- BaseFinder cannot save in ESD format. So, the first time
the user tries to save an ESD file after opening, the save
panel will come up, requiring the choice of a new format.
Version 4.0b1 11/29/00 - This is the first
public release for MacOS X Public Beta.
Changes
- Removed all uses of PS and DPS functions, and replaced
with NSBezierPaths
- Made changes to (hopefully) improve drawing speed of
bases shown on traces.
- Updated Icons for OSX
- Fixed various bugs
- Updated progress bar to use OSX style "barber pole"
Issues
- See the GeneKit HISTORY file regarding questions about
two of the files used there.
- Printing has only had cursory testing, so may or may not
work at present.
Known Bugs
- Multiple bases can be selected in Bases panel. This
shouldn't be the case, but was necessary to work
around an apparent bug in OSX/PB.