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?
0
1 reply to this topic
#2
fishdoc
-
- Active Members
-
- 272 posts
Veteran
2
Neutral
Neutral
Posted 01 October 2010 - 06:26 AM
hianghao, on 01 October 2010 - 06:03 AM, 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...alw2/index.html
