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>> Sequence Variability Server

INPUT FORM

This server calculates the variability in each column of a multiple sequence alignment using the Shannon entropy (H) function. H values range from 0 (only one residue in present at that position) to 4.3 (all 20 residues are equally represented in that position).

Sequence variability is then plotted against the selection of either consensus sequence, first sequence, or most abundant sequence in the alignment.

In addition, the server allows the user to set a Shannon Filter in order to search the alignment for sequence stretches with variability (Shannon Entropy, H) under the set value. For more detail information click here

Alignment name:

Upload your alignment file (CLUSTAL format), or

Paste your alignment. Remember in CLUSTAL format CLUSTAL W (1.81) multiple sequence alignment C_AF286225 LLEVSQNQQENNERDLLALDS-KNLWNWFNITNWLWYIK C_U46016 LLEVSQNQQDKNEKDLLALDKWENLWNWFNITNWLWYIK C_U39250 LLEESQNQQENNEKDLLALDKWQNLWSWFDITKWLWYIR C_U39251 LLEESQNQQENNEKDLLALDKWQNLWSWFDITKWLWYIR C_AF286234 LLEESQTQQENNEKDLLALDKWNSLWTWFDITKWPWYIK C_AJ276221 LLEESQNQQENNEKDLLALDSWKNLWSWFDITKWLWYIK C_AF067155 LLEESQNQQEENEKDLLALDSWKNLWNWFDITKWLWYIK C_AF286223 LLEESQIQQEQNGKDLLALDSWQNLWNWFSITKWLWYIK C_AF286224 LLEDSQSQQEQNEKDLLALDSWNNLWNWFDITKWLWYIK C_AF110969 LLEVSQNQQEQNEKDLLALDSWQNLWSWFDISKWLWYIK C_AF110970 LLEVSQNQQEKDEKDLLALDSWQNLWNWFDIPKWLWYIK C_AF110971 LLEVSQNQQEKNEKDLLALDSWKNLWNWFDISKWLWYIK C_L22946 LLEVSQNQQEKNEKDLLALDSWGSLWNWFDITKWLWYIK C_U08454 LLEDSQNQQEKNEKDLLALDSWNNLWNWFNITKWLWYIK C_AF110962 LLEDSQNQQEKNEKDLLALDSWNNLWNWFGITKWLWYIK C_AF219270 LLEESQNQQEKNEKDLLALDSWESLWNWFNITKWLWYIK C_AF219269 LLEESQNQQEKNEKDLLALESWDNLWNWFNITKWLWYIK C_L22944 LLEESQNQQEKNENDLLALDNWNNLWNWFNITKWLWYIK C_AF067157 LLEDSQNQQEKNEKDLLALDSWKNLWSWFDITNWLWYIK C_AF067159 LLEDSQNQQEKNEKDLLALDSWKNLWSWFDITNWLWYIK C_AF067158 LLEDSQNQQEKNEKDLLALDSWKNLWSWFDITNWLWYIK C_AF286227 LLEDSQTQQEKNEKDLLALDSWKNLWSWFDISNWLWYIK C_AB023804 LLEESQNQQEKNEKDLLALDSWKNLWSWFDITNWLWYIK C_AF219263 LLEESHIQQEKNEKDLLALDSWRSLWTWFDITNWLWYIK C_AF110960 LLEESQTQQEKNEKDLLALDSWQNLWNWFSITNWLWYIK C_AF110961 LLEESQTQQEKNEKDLLALDSWQNLWNWFSITNWLWYIK C_AF110959 LLEESQTQQEKNEKDLLALDSWQNLWNWFSITNWLWYIK C_AF110968 LLEESQNQQEKNEKDLLALDSWQNLWNWFSITNWLWYIK C_AF110967 LLEESQNQQEKNEKDLLALDSWQNLWNWFSITNWLWYIK C_AF110976 LLEESQNQQEKNEKDLLALDSWNSLWNWFSITNWLRYIK C_AF110978 LLEESQNQQEKNEKDLLALDSWNSLWNWFSIVNWLRYIK C_AF110977 LLEESQNQQEKNEKDLLALDSWNNLWSWFSIANWLWYIK C_AF286232 LLEESQYQQERNEKDLLALDSWKNLWDWFNISNWLWYIK C_AF321523 LLEESQNQQERNEKDLLALDSWKTLWSWFDISNWLWYIK C_AF110974 LLEESQNQQEQNEKDLLALDSWNNLWSWFNISNWLWYIK C_AF110975 LLEESQNQQEQNEKDLLALDSRNNLWSWFNISNWLWYIK C_AF110973 LLGESQNQQEQNEKDLLALDSWNNLWSWFNISNWLWYIK C_AF110972 LLEVSQNQQEQNEKDLLALDSWANLWNWFNISNWLWYIK C_U39239 LLEVSQNQQEENEKDLLALDKWQNLWSWFNISNWLWYIK C_U39242 LLEVSQNQQEENEKDLLALDKWQNLWSWFNISNWLWYIR C_AF286233 LLEVSQNQQEENEKDLLALDNWNILWSWFNITNWLWYIK C_AF110980 LLEESQNQQEKNEQELLALDSWANLWNWFAISNWLWYIK C_AF110981 LLEESQNQQEKNEQELLALDSWANLWNWFAISNWLWYIK C_AF110979 LLEESQNQQEKNEQELLALDSWANLWNWFAISNWLWYIK C_AF290027 LLGESQIQQEKNEKDLLALDSWKNLWSWFSITNWLWYIR C_AF290030 LLGESQIQQEKNEKDLLALDSWKNLWSWFSITNWLWYIR C_AF219266 LLEDSQIQQEKNEKDLLALDSWENLWSWFNITNWLWYIR C_U39237 LLEESQNQQEKNEQDLLALEQWQNLWSWFSITNWLWYIR C_U39248 LLEESQNQQEKNEQDLLALEQWQNLWSWFSITNWLWYIR C_AF286231 LLEDSQTQQERNEKDLLALDNWKNLWNWFSITNWLWYIK C_AF268277 LLEDSQNQQERNEKDLLALDNWKNLWSWFDITNWLWYIR C_AF067154 LLEDSQNQQERNEKDLLALDSWESLWNWFSISKWLWYIK C_AF219264 LLEDSQNQQEKNEKDLLALESWENLWNWFSITQWLWYIK C_AF110964 LLEDSQNQQEKNEKDLLALGSWDSLWNWFGITNWLWYIR C_AF110966 LLEDSQNQQEKNEKDLLALGSWDSLWNWFGITNWLWYIR C_AF290029 LLEDSQNQQEKNEKDLLALDSWKNLWNWFGITNWLWYIK C_AF290028 LLEDSQNQQEKNEKDLLALDSWKNLWNWFGITNWLWYIK C_U08453 LLEDSQNQQEKNEKDLLALDSWKNLWNWFDITNWLWYIK C_AF219274 LLEDSQNQQEKNEKDLLALDSWKNLWNWFSITNWLWYIK C_AF110963 LLEDSQNQQEKNEKDLLALDSWNNLWNWFSITNWLWYIK C_AF110965 LLEDSQNQQEKNEKDLLALDSWNNLWNWFSITNWLWYIK C_U08455 LLEDSQNQQERNEKDLLALDSWNNLWNWFNITNWLWYIK C_U39233 LLEDSQNQQEQNEKDLLALDKWQNLWSWFDITNWLWYIK C_U39252 LLEDSQNQQEQNEKDLLALDKWQNLWSWFDITNWLWYIK C_U39241 SLEDSQTQQENNEKELLELDKWQNLWSWFDITNWLWYIK C_U39243 LLEDSQTQQENNEKELLELDKWQNLWSWFDITNWLWYIK C_L23065 LLEVSQTQQEQNEKDLLALDKWQNLWSWFDITKWLWYIK C_U39234 LLEDSQNQQEKNEQDLLALDKWQNLWNWFDITKWLWYIK C_U39238 LLEDSQNQQEKNEQDLLALDKWQNLWNWFDITKWLWYIK C_AF286228 LLEDSQNQQKKNEQDLLASDKWQNLWSWFDITKWLWYIK C_U39240 LLEDSQNQQEKNEQELLALDKWQNLWNWFDISKWLWYIR C_U39257 LLEDSQNQQEKNEQELLALDKWQNLWNWFDISKWLWYIR C_AF286235 LLEDSQKQQEKNEQELLALDKWQNLWNWFSITKWLWYIK C_L22940 LLEDSQNQQEKNEQDLLALDKWQNLWNWFSITKWLWYIK C_L22948 LLEDSQNQQEKNEKDLLALDKWQNLWSWFDITKWLWYIK C_U39245 LLEDSQNQQEKNEEDLLALDKWQNLWNWFGITNWLWYIK C_U39247 LLEDSQNQQEKNEEDLLALDKWQNLWNWFGITNWLWYIK C_U39249 LLEDSQNQQEKNEEDLLALDKWQNLWNWFGITNWLWYIK C_U09126 LLEDSQNQQEKNEQDLLALDKWQNLWTWFGITNWLWYIK C_U15121 LLEDSQNQQEKNEQDLLALDKWQNLWTWFGITNWLWYIK C_U52953 LLEDSQNQQEKNEQDLLALDKWQNLWTWFGITNWLWYIK C_U39244 LLEVSQNQQEKNENDLLALDKWQNLWNWFSITKWLWYIK C_U39246 LLEVSQNPQEKNENDLLALDKWQNLWNWFSITKWLWYIK C_AF219262 LLEVSQNQQEKNEKDLLALDKWQNLWNWFGITKWLWYIK * *: *..: .:** . ** ** * :* **:

OPTIONS

Output Sequence:

Consensus sequence:
Threshold: 55% 70% 80% 90%
Most abundant sequence
First sequence in alignment

Shannon Filter:

Shannon Entropy Threshold

Fragment Length

Enhanced PVS Tool available at Dr. Reche Immunomedicine Group

For questions about this site: Pedro A. Reche

Credits

Shannon Entropy calculations Rob Meijers

Shannon filter and web programming by Pedro A. Reche

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