Mac Sequence Viewer Help
Thank you for choosing Mac Sequence Viewer - the only program that allows you to generate quality reports using your Macintosh Computer. We have designed this program to run quickly and efficiently - like your Mac.
Running Mac Sequence Viewer
Simply drag your AB1 files onto the program icon. Within seconds, the program will generate an easy to read report for you that includes the following data:
- Quality scores for each read (assigned by ABI on a scale of 0 to 60. 60 is the best; 0 is the worst). Quality scores can be used to weed out poor quality runs. They can also be used to sort reads from high quality to low quality - thereby allowing you to select the best clones / PCR products.
- A graphical depiction of the ratio of high, medium, and low quality bases (high quality bases are the green bars; low quality bases are the red bars). Knowing the ratio of base quality is very useful. If you have a short PCR product, the length of read may be short... Initially, you may be inclined to consider this a bad run.. but if you look at the graphical representation of the quality ratio, you will quickly see that most of the bases are good - making this a quick screening method for quality.
- A numerical (and color coded) representation of the Signal to noise ratio. A green background means that the signal strength is fine. A yellow background indicates that the signal strength is borderline. A red background indicates that the signal strength is unacceptable. This information gives you a quick idea of WHY the read may have problems. If it is weak, and the quality is low, you may decide that the reaction did not go well. If it is strong, and the quality is low, that is a strong indicator that the sample produced mixed sequence (two or more sequences super-imposed). Looking at the chart in this way can help you quickly assess if you picked two colonies, or if there was contamination.
- A graphical and numeric representation of the Read Length. This is useful in seeing how many bases were called. You can sort every column by clicking on the column headers. Doing this will enable you to sort out the shortest reads (and perhaps weed them out).
- A colored and numeric representation of the Base Spacing. In some cases, alternative sequencing chemistries can cause the bases to migrate differently through the matrix. Using this report, if you find that the base spacing is off (red background) you can quickly single out runs that were affected by a spacing problem. Spacing problems can often be fixed by re-sequencing - especially with a different chemistry.
Chromatogram Viewer
Do you need to view the chromatogram (the trace file with the 4 color peaks)? In the report, every sample name becomes a link. When you click the link, a new window will pop up displaying the chromatogram file. This is very useful when you are trying to determine if a base mismatch is real or an artifact. This view is especially useful for researchers who are looking for SNPs (Single Nucleotide Polymorphisms). If this feature is not working on your computer, please be sure that you have javascript enabled, and that you are allowing pop-up windows in your web browser.
FASTA file generation
Do you need to create a FASTA file for use in other programs? No problem - simply click the link in the upper right hand corner that says FASTA. A FASTA file will immediately appear in your browser window. You can save this file from the browser... or you can use your right mouse button (control and click if you only have one button) when clicking on the FASTA link. You will be given a message box that asks what you want to do. Choose "Save Linked File to Disk," and the FASTA file will be immediately saved on your desktop.
Quick Links
We provide quick links to BLAST and VecScreen. These links go through our proxy server, so we update them as they change. No more searching around for BLAST and VecScreen on the web.
Sortable
Remember, every column is sortable when you click on the column header (the part with the gray background e.g. No., Cap No, Sample Name, Sample Comment, etc..) Sorting runs by quality or name allows you to quickly make decisions about your work and your samples. No other program for the Mac offers this detailed, useful quality analysis report.