Dear Sir/Mam ,
I have one problem in my research work, I am trying to align 4.5MB large DNA sequence. Could any one suggest any tool for pairwise alignment of this large sequence.
Currently I am using Vista tool, but its result is very complicated.
ncbi BLAST will handle large input sequences but upload/input times are long so it may be worth trying input of contiguous 500kb fragments or smaller to get the results back quicker
Yes sir, I face this problem during NCBI BLAST search.
thank you sir for your suggestion.
How was the genome sequence generated. If it is generated by whole genome sequencing, then there are other methods to analyse the data and annotate the resulting assembly. It need not to be complete, but thats the way to go.
What result do you expect for a whole genome blast?
(And make sure if it is 5.4MB or 4.5MB)
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