Hi, can someone help me to do multiple sequence alignment and get features like N-glycosylated, PKC as well as unsp sites? I saw Madam Suzanne recommended someone to use Jalview, but I can't use it as it contains sequences and is not editable. Thanks in advance.
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Bablee •
1 answer
There are two questions here, not necessarily related.
There are several software for doing multiple sequence alignment e.g Clustal Omega, MUSCLE, MAFFT, T-Coffee and others.
To get annotated features on a given sequence, you should use relevant databases. If you want to make predictions of specific sites, then there are also dedicated tools for different types of sites, e.g. see omics tools for post-translational modifications.
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What are "unsp" sites ?
Unsp is unspecified protein site
What is an unspecified protein site ?
In amino acid sequence there are many types of sites like casein kinase II phosphorylation sites, protein kinase C phosphorylation sites (PKC) and many others, so unsp is denoted as unspecified site may be its name and function is still unknown.
What does that mean? What contains sequences and is not editable?
From JalView site:
Which seems to be what you want to do.
I want to do multiple sequence alignment, but the desktop version of Jalview that I downloaded contains the list of sequences and feredoxin information. So I don't know how to clear and put my sequences to be executed.
Check out the training videos for JalView. The list is extensive and should address all of your needs.