After carrying out automatic alignment on a set of proteins (e.g using MAFFT, Muscle, ClustalOmega), it is often necessary to manually edit the alignment.
What is the basic principle behind such manual editing? What should one be looking for in the MSA to manually correct?
Are there any tutorials or articles on how to carry out such manual alignments?
The data set may be very large (I have 1520 proteins). Will I need to visually inspect the entire dataset? Can a script (e.g python) be used to look for errors and also to 'manually' edit those errors? Or are there any bioinformatics software that can suggest what sites need manual adjustments?
P.S: I am new to bioinformatics research and manual alignment is something I hear everyone say they did but no one explains how they did it!
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jscience •
1 answer
See my answer to a similar question here.
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Is this a real request or is this something for an assignment?
1: Humans are better at understanding context of sequence data and can look at the entire alignment when making decisions. You should be looking for excessive/oddly spaced gaps for starters.
2: I think you meant to ask "editing" than alignments. Any editing you do needs to be within reason (that is a rather fluid bar that you will have to set for yourself).
3: Is there redundant data in that set that can be eliminated?
You can use MEGA, JalView, SeaView to do the actual editing.
Thank you.
Using UGene, it is possible to remove columns with more than a specified threshold of gaps. I used 99% (so columns with more than 99% gaps are removed). Does this achieve the same result?