How to compare more than 2 nucleotide fragments? - I used blast and it returns no similarity (Oct/01/2010 )
I've got 4 highly similar nucleotide fragment and i wish to design specific primers for each of them. Their protein coding are about ~80% similar. I tried to use blastn (NCBI): align 2 sequences (megablast, discontinuous megablast, balstn) and pasted in 2 of my sequences. And the result was: no similarity for both megablast, and ~70% similarity for blastn from 112 to 253. The thing is, by looking directly at 2 sequences, the similarity started from 1st base, not base 112! Did i somehow altered the setting or what happened? How should i align more than 2 sequences together so that i can have a clear look on them?
-hianghao-
hianghao on Fri Oct 1 14:03:54 2010 said:
I've got 4 highly similar nucleotide fragment and i wish to design specific primers for each of them. Their protein coding are about ~80% similar. I tried to use blastn (NCBI): align 2 sequences (megablast, discontinuous megablast, balstn) and pasted in 2 of my sequences. And the result was: no similarity for both megablast, and ~70% similarity for blastn from 112 to 253. The thing is, by looking directly at 2 sequences, the similarity started from 1st base, not base 112! Did i somehow altered the setting or what happened? How should i align more than 2 sequences together so that i can have a clear look on them?
clustal
http://www.ebi.ac.uk/Tools/clustalw2/index.html
-fishdoc-