Hi everyone
I have very simple question about how to operate blast.
so I have blast a sequences against it's reference genome, and I got two inversion at certain region shown in dot plot:
I am wondering, is it able to ask BLAST to come results that shows the break points when align the sequences?
In this case:
I want the output to be strand plus/plus
Query 1----------- 900,000
Subject 1 --------------900,000
strand plus/minus Query 900,001----------- 1,250,000 Subject 900,001 --------------1,250,000
strand plus/plus
Query 1,250,001----------- 3,400,000
Subject 1,250,001 --------------3,400,000
strand plus/minus Query 3,400,0001----------- 4,200,000 Subject 3,400,0001 --------------4,200,000
strand plus/plus Query 4,200,000----------- 4,411,532 Subject 3,400,0001 --------------4,411,532
I don't know if this is possible with local alignment but what I am envisioning if it can create dot plot like this it should be able to do it. So it is still local alignment but make the length to max til where the break point is. I don't care about sequence identity too much because I want to know where the break point happens in the query sequences.
I prefer command line input if it is available.
Thank you
If the sequence identity around break point is low, you can't be sure of the exact location of the break point. Your best approach would be to consider the interval delimited by the high similarity extremes.
You could also try Mauve, I think it tries to include the complete sequences on its output.
thanks for reply
The reason I want use blast is it is fast. Mauve takes a very long time and its output is still unclear.