DNA sequence alignment

[Peter Ellis]

Look at the alignments!  Compare what BLAST does to what ClustalW does. 
  Check the orientation of your sequences.  BLAST will try both forward 
and reverse, ClustalW assumes you're giving it the sequences the same 
way round. That might be why BLAST "sees" the similarity while ClustalW 
aligns them wrongly.

Best wishes,
Peter

On 5/18/2012 10:43 AM, Elyaseen Daniel wrote:
> Dear listers,
>
> Hello!
>
> I have sequnced a DNA fargment (PCR product) then BLASTed the sequnce (in NCBI BLAST). I got 97% similarity with a named species. I took my sequence and the six closest sequences and aligned them (Clustal W) then conducted a phylogeny analysis using MEGA 5 (using Neighbour-Joining with p-distance). The tree showed that my sequence is far from the one with 97% similarity (a really far clade!). If I do not align the sequences and run the same phylogeny analysis I get my sequence and the one with 97% similarity in ONE clade supported by a high bootstrap value (86%). Any explanations on why the alignment is making this change. (by the way I tried alignment with MUSCLE or doing Maximum Likelihood but that did not slove the problem).
>
> Thanks a mellion.
>
> Elya