Hi everyone..i just want to ask..how to analyse raw dru sequence of Staphylococcus species for dru typing identification of Staphylococcus species?..I already read several journals and they suggest to used TRST sequence analysis software from Bionumerics software and dru repeat analysis using manually can be a challenge. So..really mean that, typing using dru sequence require bionumerics software and can't used manually?...
Thank you
Of course you can do it manually, you can fill in the sequence of each individual repeat in the dru-typing website to obtain the type.
If you want to cluster based on the dru-types, you will need to first calculate a similarity between each isolate (after pairwise aligning the repeats) based on a cost table between all different repeat types, and then make a dendrogram or tree based on the similarities.
The reason why these articles suggest the use of BioNumerics is not because it is impossible without, but because the analysis of many samples on a routine basis, would take so much time that it becomes cheaper to buy the license to the software that autaomates this. If you however have a limited dataset for a one-time analysis, you can definitely just analyse them manually.
http://www.dru-typing.org/site/search2.php
Thank you for the suggestion..i'm deal with 38 isolates and i think i need that software to obtain the result. Another problem is i can't find this consensus dru sequence (ATAAGAGGTA CGTTAAAAGC AGTTCTAAGT AAAAT TGCAG ) from my dru sequencing result?. I did PCR by using primers that suggested from dru-typing website and i get expected band size around 900bp. I sequence using same primers to obtain the sequence result..
did you sequence both forward en reverse? How long is your assembled contig?
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