bioedit vs blastn results
 

hello, I have blasted my contigs and obtained some hits with high percentage identities. I then retrieved the fasta files of those hits and computed sequence identity matrix using bioedit. I expected the results from both blastn and bioedit to be the same, but they are not. Is this proper? if Not, what could be the problem?

I have attached a doc showing results

What exactly are you trying to do?

Blastn hits are probably not full length (unless the sequences are very homologous from end-to-end). I assume you are importing sequences that are full length into bioedit and then aligning them with clustalW (which is now a global alignment instead of the local in Blast). That is probably the reason why your identity matrix is not showing values closer to 1.0.

hi,

My interest is to generate a Pairwise sequence comparison matrix.
the blastn hits include both full length and partial. Seq identity matrix I posted were generated without clustalw alignment. when I aligned only 3 long seqs out of the 12 seqs remained. Imagine the 9 were eliminated because of being short?,dissimilar?

Are these sequences of similar length? Are there repeats (internal)?

You may want to look at dot plots if you are trying to find similarities.

The sequences differ in length. I have not checked whether there are repeats. how do I check for repeats?

I will read about dot plots using the link provided.

thanks