bioedit vs blastn results

[kaps]

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

[GenoMax]

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.

[kaps]

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?

[GenoMax]

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.

[kaps]

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