bioedit vs blastn results

kaps · 05-31-2015, 11:52 PM

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 · 06-01-2015, 04:32 AM

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 · 06-01-2015, 07:02 AM

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 · 06-01-2015, 07:18 AM

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 · 06-02-2015, 06:37 AM

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

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06-01-2015, 04:32 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,083	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.

06-01-2015, 07:02 AM	#3
kaps Member Location: Uganda Join Date: Jan 2015 Posts: 71	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?

06-01-2015, 07:18 AM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,083	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.

06-02-2015, 06:37 AM	#5
kaps Member Location: Uganda Join Date: Jan 2015 Posts: 71	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