Dear All,
My Question is It ABI files are necessary for MLST analysis ? I lost My data regarding Forward Read sequences I can make its complementary sequences but one of my friend told me Abi / Chromatogram files are mandatory please guide me if any possible solution for this problem ... Many thanks in ADVANCE..
Dear Muhammad Umar Zafar Khan
if you have reverse read sequences maybe they will be sufficient (long enough to cover the gene of interest). Try to upload it to a MLST database (e.g. https://pubmlst.org/databases/ ) if your bacterial species which you investigated is in the list. Very soon you will see if you have whole gene covered or not.
Anyway, for working with MLST databases, *abi file is not mandatory, you can also use a sequence if you have it but as a researcher you should have your raw data stored for at least five years after publication of your results.
Try to contact sequence facility, maybe they have your data stored.
Good luck,
Marcela
My Most Respectable Madam,
thanks alot for alot your kind words.
I am ist person who develop the scheme of my organism and using 11 HKGs.
my data of sequences is sufficient to identify the specific genes. but confusion is that how find STs and analysis of data , will be By any software like Bionumeric or pbmlst can help to analysis of final results .
Seeking for your guidance pl.
Umar
Umar
A sequence type is determined by a combination of alleles (variants) of housekeeping genes. If you have a full gene sequence covered and you are the first who described this MLST scheme for a new bacteria, you can determine your own sequence types (ST) as a combination of gene alleles you identified. Bionumerics or Geneious are fine for visualisation and comparison of sequences. To show how the strains are related you can use MEGA software. The MLST puborg database can be used only for previously described MLST schemes of several bacterial species.
Best,
Marcela
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