I have retrieved 750 aa sequences of a protein from Uniprot having variable length ranging from 180 to 1293 aa. I want to shortout sequences which have length more than 1000 aa. Kindly help me.
I do not know if I understand your question. Do you want only a portion of the protein that resembles that of 750? If so, you can align all proteins and after alignment, manually delete the non-aligned portions, that is, larger than the desired size.
If you are aligning remember to not allow insertion of gaps, and / or aligning taking your sequence as a reference to the others.
My question is I have downloaded 750 aa sequences of various length ranging from 180 to 1293 aa long. But now I want to do MSA for only those sequences which are longer than 1000 aa. So, how to remove sequences which are shorter than 1000 aa.
Dear, unfortunately, I do not know how to help you. I would do manual, but I understand it is impractical. Through command lines in unix, maybe you can do it. Try contacting bioinformatics forums.
I'm sorry I could not help you.
If you can, please explain to us how you can do it.
Good luck
Currently I'm doing it manually in MEGA and BioEdit, but i think it can be done in a single command by using python.
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