AVG

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Altuntas, Levent

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Mar 12, 2021, 5:58:39 AM3/12/21
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Hi Guys,


i use TCS and ask myself what does the AVG yellow symbol stand for? I think BAD and GOOD is clear, here the score is good or bad. Is AVG for a middle score? I did not find a register to read about all symbols like *. _ below the multiple sequence alignment. What dos CON mean?


Best wishes

Levent

Chang Jia-Ming

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Mar 13, 2021, 10:24:50 AM3/13/21
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Dear Levent,

Altuntas, Levent <levent....@rwth-aachen.de> 於 2021年3月12日 週五 下午6:58寫道:

Hi Guys,

i use TCS and ask myself what does the AVG yellow symbol stand for? I think BAD and GOOD is clear, here the score is good or bad. Is AVG for a middle score?

yes, if we rank the confidence of the alignment from 0 to 9, AVG corresponds to around 5.
One example alignment @ http://tcoffee.crg.cat/data/eba4fd07/result.score_html
its raw score @ http://tcoffee.crg.cat/data/eba4fd07/result.score_ascii
The 1th~4th amino of the sequence 1aboA => yellow, AVG, raw score (ResidueTCS) = 4~5 

I did not find a register to read about all symbols like *. _ below the multiple sequence alignment.

What dos CON mean? 

The color code of CON shows the score of ColumnTCS.
Its label is described in  Figure1 @ Taly, J.-F. F. et al. Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures. Nature protocols 6, 1669–82 (2011).
"Asterisk (*), conserved amino acid in all sequences. Colon (:), a position of the MSA composed of residues having the physicochemical properties. Dot (.) indicates the column of the MSA for which semi-conserved substitutions are observed."

Regards,
Jia-Ming Chang 張家銘


Altuntas, Levent <levent....@rwth-aachen.de> 於 2021年3月12日 週五 下午6:58寫道:
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