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Dear all,
Our group need to build a sequence alignment of some short reads (archaeal 16S rDNA sequences generated by pyrosequencing on 454).
To do so, we selected the ones we needed to check and aligned them on the SINA aligner to retrieve the closest relatives using the archaeal profile. We then also collected some 16S sequences from the SILVA database from reference archaeal groups (e.g. MGI, MBGs etc), added an outgroup sequence, put everything together and aligned them using MUSCLE.
The resulting trees are all very poor, in terms of quality. We though that it might be due to the fact that our own sequences are quite short, compared to the reference ones (ca. 500 bps vs often more than 1200), thus I'd like to extract the portion of the alignment including our sequences and realign it before rebuilding the respective tree.
Would it be correct, in your opinion?
Best
Michael Tangherlini
Our group need to build a sequence alignment of some short reads (archaeal 16S rDNA sequences generated by pyrosequencing on 454).
To do so, we selected the ones we needed to check and aligned them on the SINA aligner to retrieve the closest relatives using the archaeal profile. We then also collected some 16S sequences from the SILVA database from reference archaeal groups (e.g. MGI, MBGs etc), added an outgroup sequence, put everything together and aligned them using MUSCLE.
The resulting trees are all very poor, in terms of quality. We though that it might be due to the fact that our own sequences are quite short, compared to the reference ones (ca. 500 bps vs often more than 1200), thus I'd like to extract the portion of the alignment including our sequences and realign it before rebuilding the respective tree.
Would it be correct, in your opinion?
Best
Michael Tangherlini