September 4, 2007 at 9:30 am #978resnantiParticipant
i wonder how does long trace software work with ab1 file? thx
September 14, 2007 at 9:31 am #979DanielKeymaster
How LongTrace works is a trade secret, but in general terms it does the same type of processing that ABI’s software does only we are better at it than ABI. I know these seems strange as the guys at ABI are pretty smart. I suspect the ABI management doesn’t think it is a priority to improve the processing of their own traces and hence the software people there don’t work on it.
In the end it doesn’t really matter – what matters is does LongTrace improve your own traces and the best of finding that out is trying our free LongTrace DNA sequencing service. Hopefully you will like what you see 🙂
You might also want to check out our new basecaller PeakTrace. This works much like LongTrace, but on a wider range of machines (it can even improve ABI 377 trace). You can also try it for free at the PeakTrace DNA sequencing basecaller page.
September 20, 2007 at 9:35 am #980miraParticipant
I tried putting my sequences for the free LongTrace DNA sequencing service. My seq were in the correct ab1 format but i only got this reply ‘Weak or failed trace’. Can you help me out? For your info, the sequences i put in is about 800 bp in length.
Also can you explain a bit about the 10 trace limit per person? What does the term ‘trace’ refer to?
I’m rather new at this and i’de like to understand more if its not too much trouble.
Thank you 🙂
September 20, 2007 at 9:40 am #981DanielKeymaster
If your trace is giving “weak or failed” traces at the end it means that the signal at the end of the trace is too low to be improved by LongTrace. I can’t really tell you much more without seeing you trace, but if you open you trace in a trace viewing program like FinchTV you can have a look at the signal at the end of the trace. You need to look at the raw data as this is what LongTrace uses to do the basecalling. If the peak signal at the end of the trace is very weak (basically flat) then LongTrace is not able to do much to improve the basecall.
A trace file is just the ab1 file that contains the sequence data peaks. I don’t really know why they are called trace files – I guess there is some sort of historical reason for it.
The free service has a limit of 10 files per day – it is really only for tiny users and people wanting to try LongTrace. If you want to process more files then this you need to register for LongTrace FTP.
Finally, have you tried PeakTrace too? Sometimes it is able to improve traces that can’t be improved by LongTrace. The link for the free PeakTrace version is here:
- This reply was modified 4 years, 3 months ago by Daniel.
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