Chromas Help Contents

Acknowledgements
Disclaimer
Using Chromas

Chromas menu commands

File
Edit
Options


Acknowledgements

Chromas was inspired by ABIView, by David H. Klatte. I would like to thank all the people who have made suggestions for Chromas since it was first released in 1996. Thanks also to Dr. Clark Tibbets for writing his paper "Raw Data File Formats, and the Digital and Analog Raw Data Streams of the ABI PRISM(tm) 377 DNA Sequencer" and making it available on the Internet.


Disclaimer

Chromas comes with no guarantee of reliability or suitability for a particular purpose. I have tried to make it as reliable as possible, but you use this software at you own risk. Always backup your data.

I have no "inside" knowledge of the ABI file format, only what has been found by reverse engineering. There may be some ABI chromatogram files with which Chromas will not work properly or at all. If you have an ABI chromatogram which you think Chromas should work with but doesn't, email it to me at conor@technelysium.com.au and I will see what I can do.


Using Chromas

Chromas displays the chromatogram files from Applied Biosystems automated sequencers, and files in the Staden SCF format. Chromatogram files can be transferred from a Mac to a PC over a network or by using a Mac program capable of writing to DOS/Windows disks, or a DOS or Windows program capable of reading Mac disks. All PowerMacs can write to DOS/Windows disks.

Incorrect basecalls selected using the mouse can be changed or deleted accordingly. Holding down the backspace or delete keys will rapidly delete succesive bases, backwards for backspace and forwards for delete. Once a base is selected, you can scroll through the sequence using the left and right arrow keys. Click between bases to insert. The edited sequence can be copied to the clipboard or exported to a file.


File Menu

Open

Open an ABI or SCF chromatogram file. If you select more than one file, new windows will be opened to display the files.

Save

Save an SCF chromatogram file. If an ABI chromatogram file is loaded, this option is grayed.

Save As

Save the chromatogram file under a new name. You can use this option to save ABI chromatograms in SCF format.

Export

Export the sequence to disk as a single line of plain text, or in FASTA format.

Export Raw Data

Export the chromatogram trace data as a text file with four columns of Y-coordinates.

Print Options

Allows you to set the X and Y zoom factors for the printout. These are independent of the settings for the display.

Print

Print the chromatogram. The printout looks similar to one from ABI's software. The zoom factors for the printout are set using the Print Options menu (see above). Don't forget to set the orientation to landscape, unless you want it printed in portrait. By default, only the first page is printed. You should only need to change this if your runs are readable past about base 600.

New Window

Runs another instance of the application and positions its window above or below the existing one, if there is room. Use this for comparing two or more chromatograms.

Exit

Causes a can of beer to be ejected from drive A.


Edit Menu

Undo

Undo up to 100 changes to the sequence.

Copy sequence to clipboard

Copy the sequence to the clipboard as a single line of plain text, or in FASTA format.

Reverse Complement

Reverse and complement the sequence and chromatogram.

Next N

Find the next "N" after the currently selected base. You can also use Ctrl-N.

Next Redundant

Find the next redundant nucleotide code after the currently selected base. You can also use Ctrl-R.

Find

Search for a particular sequence. Click Find to find the first occurrence of the sequence, and Find Again to find subsequent occurrences. The search is case insensitive and the following redundant codes can be used in the string:

B	Not A
D	Not C
H	Not G
K	G or T
M	A or C
N	G,A,T,C
R	A or G
S	C or G
V	Not T
W	A or T
Y	C or T

If found, the first base of the sequence is selected.


Options Menu

X Zoom

Zoom in or out on the X-axis. Fit To Window displays the whole chromatogram, with no sequence.

Y Zoom

Zoom in on the Y-axis. Note: as of v1.42, this no longer sets the Y-axis zoom for printing the chromatogram. This is done in Print Options in the File menu.

Y scale

Choose a small or large Y-axis scale.

Font Size

Choose a small or large font size for the file information, sequence and numbering. This might not change the size of the sequence and numbering font, even though it does change the size specified to Windows when the font is created (blame Windows).

Colors

Set the colors for the bases and gel traces.

Continuous Edit

When this option is checked, changing a selected base will cause the next base in the sequence to be selected.

Original Sequence and Edited Sequence

ABI chromatogram files contain two copies of the sequence - the original sequence produced by the analysis software, and an editable copy which can be changed using ABI editing software. You can select which sequence to display. Note that when you change which sequence is displayed, any changes to the previously displayed sequence cannot be undone using the Undo command. When saving or exporting, the currently displayed sequence is used. SCF files contain only one copy of the sequence, so these options are grayed when an SCF file is loaded.