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How to compare more than 2 nucleotide fragments?


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#1 hianghao

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Posted 01 October 2010 - 06:03 AM

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?

#2 fishdoc

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Posted 01 October 2010 - 06:26 AM

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




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