sequence analysis - (Feb/10/2007 )
Suggestions please
I have sequenced 20 strains of Xanthomomnas campestris for the hrp gene.
Upon BLASTing, the type strain genome sequence produced an identity however aligning this sequence with my sequnces I end up with an approximate gap of 100bp. How could this be possible? Within my strains sequences there are at least 7 Xanthomonas reference strains?
Could there be something with my primer design?
-shia-
Could it be an intron? Alternative splicing?
What are you sequencing? cDNA, genomic DNA, plasmid, bac, pac? How many primers did you use? Were you sequencing PCR products? Did you sequence using both the forward and reverse primers? And did all strains contain the exact same gap (down to the last nucleotide)
-perneseblue-
QUOTE (shia @ Feb 10 2007, 09:49 PM)
Suggestions please
I have sequenced 20 strains of Xanthomomnas campestris for the hrp gene.
Upon BLASTing, the type strain genome sequence produced an identity however aligning this sequence with my sequnces I end up with an approximate gap of 100bp. How could this be possible? Within my strains sequences there are at least 7 Xanthomonas reference strains?
Could there be something with my primer design?
En, from technical point of view, you might want to check you blast options, look specifically for:
1. whether low complexity regions are masked.
2. repeat sequence masking.
Otherwise, could be more complicated biological reasons.
-cyberpostdoc-