Hi,
Our lab is currently sequencing a 1000pb gene fragment. They sequence foward and reverse strand, so they get the same strand sequenced twice. Reverse output is processed in order to get reverse complementary. Then a needlemann alignment is done between forward and reverse complementary. One of the strands from needle output is cuted handly without an standard criteria and this is called 'consensus sequence'.
Can you actually do a consensus from 2 sequence? I guess not. Moreover, I tryed to use cons program from emboss package in order to try get a real consensus sequence from needle because i want to automatize this process. Cons command returns me an error about input file. Looking at its manual it's clearly said the input file must be a multiple sequence alignment, so far I remember, needle is not. Actually, I wonder how you can get a consensus from only 2 sequence, if there is a change in a nucleotide position both situations are represented equaly because theres only two sequences.
Is the process currently done correct?
I got the feeling it would be enought if only one strand got sequenced or if the Blastn was run twice, one for forward and the other one for reverse complementary.
What is your opinion?
Thank you
Our lab is currently sequencing a 1000pb gene fragment. They sequence foward and reverse strand, so they get the same strand sequenced twice. Reverse output is processed in order to get reverse complementary. Then a needlemann alignment is done between forward and reverse complementary. One of the strands from needle output is cuted handly without an standard criteria and this is called 'consensus sequence'.
Can you actually do a consensus from 2 sequence? I guess not. Moreover, I tryed to use cons program from emboss package in order to try get a real consensus sequence from needle because i want to automatize this process. Cons command returns me an error about input file. Looking at its manual it's clearly said the input file must be a multiple sequence alignment, so far I remember, needle is not. Actually, I wonder how you can get a consensus from only 2 sequence, if there is a change in a nucleotide position both situations are represented equaly because theres only two sequences.
Is the process currently done correct?
I got the feeling it would be enought if only one strand got sequenced or if the Blastn was run twice, one for forward and the other one for reverse complementary.
What is your opinion?
Thank you
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