User: ttubiana

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ttubiana20
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Posts by ttubiana

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python calculation of protein multiple sequence alignment
... Dear all :-) I am trying to compute the conservation score of each position of a protein multiple sequence alignment. I already used the Shannon entropy, but I am not satisfied with it since it is not similarity-based but identity only. So I thought that maybe it could be a good idea to use a su ...
conservation python alignment written 2 days ago by ttubiana20 • updated 2 days ago by Macspider3.1k
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Comment: C: Matching sequences from PDB with sequence from Alignment.
... Hei :-) I download the Fasta from PROSITE for the whole family and then I match on the Uniprot GeneName. The starting position is also in the FASTA header, but I do not want to localize the position of the amino acid in the protein, but in the alignment. Let's take for example the PDB 2DA0 (the P ...
written 9 months ago by ttubiana20
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Comment: C: Matching sequences from PDB with sequence from Alignment.
... To do it on Jalview I think I have to align the two sequences first, but if I do so, my original alignment will be changed, and Indeed I have hundred of sequence to match so it can be long with Jalview :-) The Idea behind is to be able to select a loop on a protein and then apply this selection on ...
written 9 months ago by ttubiana20
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Matching sequences from PDB with sequence from Alignment.
... Hi everyone, I need some advice: I am trying to match the residue numbers from a PDB with an alignment (from multiple sequences alignment - MSA, from PROSITE). But there are some difficulties : - The protein sequence in the MSA can be smaller than the PDB sequence - The PDB sequence can be a li ...
python sequence structure alignment written 10 months ago by ttubiana20 • updated 9 months ago by Cupton70

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