I was using pubmlst for analysis and have the following doubts about analysis
1. For MLST do we have to use the assembled contiq (F & R) always?
2. Can we use either Forward or Reverse sequences alone for analysis?
3. What to do in case of not getting a perfect allelic match for the query loci?
4. What in case if we are getting separate allelic numbers with forward, reverse and assembled sequences , which one to consider as our allelic number
5. With the allelic profiles if not getting STs
5. If a certain combination of allele IDs has not yet been seen, it has not been defined as allelic profile and you will need to submit this to the curator (but only if you are sure of the individual allele IDs).
For the other issues, I agree with Matt, and I suspect a poor quality sample, trace and/or assembly is the cause of the issues you are seeing. Insertions/deletions are very rare in these housekeeping genes
Thank you Mathew and Katleen
what can be done in case of getting gaps (1 or 2) in sequences for some loci.
Correct the assemblies.
A true gap in one of the MLST genes will be very very rare. Chances are the trace of your sequence was not of super quality. What happens often in Sanger trace files when you have two same bases next to each other, is that the peaks are not well separated (or even just form one large peak) and called as one base and not as two. This will result in a gap when you are comparing with the MLST allele sequences. So you need to check your traces, and correct these type of errors and then redo the identification of the allele.
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