Hi Members,
Please pardon me if my query seems silly. I've query for sequence alignment.
Suppose, I've 4 sequences: [ I randomly added any amino acid]
Ran clustalw2, with default settings:
Got output as:
It says, 1, 4, 2, and 3 at last. [ The order of alignment output]
My query is:
- Why 1 on top/first?
- Would the alignment have been different if, it would have said, 3,2,4 and 1 at last?
- On what criteria is the top decided?
Can I decide or change what to have the first?
From what I know, it is global alignment and should not have any impact on alignment irrespective of the placement of protein name.
Kindly throw light on this.
Please pardon me if my query seems silly. I've query for sequence alignment.
Suppose, I've 4 sequences: [ I randomly added any amino acid]
>1
WTQRPLPLKGGGGGGGGWWWDSSSHHHHHH
>2
WWWWWAAAAAWTQRPLPLKGGGIG
>3
WTQRAAWTQRPLPLKGGPLPLKGGGGGGGGWWAAAA
>4
WTQRPLPLKGGGGGWWWWWPLPLKGFFQQQ
WTQRPLPLKGGGGGGGGWWWDSSSHHHHHH
>2
WWWWWAAAAAWTQRPLPLKGGGIG
>3
WTQRAAWTQRPLPLKGGPLPLKGGGGGGGGWWAAAA
>4
WTQRPLPLKGGGGGWWWWWPLPLKGFFQQQ
Code:
clustalw2 -infile=test_seq.fasta -type=PROTEIN -output=FASTA -outfile=sampl_out.txt
>1
----------WTQRPLPLKGG-----GGGGGGWWWDSSSHHHHHH-
>4
----------WTQRPLPLKGG-----GGG-WWWWWPLPLKGFFQQQ
>2
WWWWWAAAAAWTQRPLPLKGG-----GIG-----------------
>3
----WTQRAAWTQRPLPLKGGPLPLKGGGGGGGGWWAAAA------
----------WTQRPLPLKGG-----GGGGGGWWWDSSSHHHHHH-
>4
----------WTQRPLPLKGG-----GGG-WWWWWPLPLKGFFQQQ
>2
WWWWWAAAAAWTQRPLPLKGG-----GIG-----------------
>3
----WTQRAAWTQRPLPLKGGPLPLKGGGGGGGGWWAAAA------
My query is:
- Why 1 on top/first?
- Would the alignment have been different if, it would have said, 3,2,4 and 1 at last?
- On what criteria is the top decided?
Can I decide or change what to have the first?
From what I know, it is global alignment and should not have any impact on alignment irrespective of the placement of protein name.
Kindly throw light on this.
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