Tools     Alignment Analysis   Databases   Computational Immunology   Modelling & 3D-structure     Analysis   Sequence Manipulation &     Analysis   Similarity Searches   View all Tools    Tools    >> Seqlogos Description: SeqLogos generates sequences logos from amino acid sequence alignment. Sequences logos are useful tools to visualyze sequence patterns and represent a more informative alternative to consesus sequence. 1. INPUT NAME (optional) 2. PROTEIN SEQUENCE ALIGNMENT (ClustalW or GCG format): Paste sequence CLUSTAL X (1.81) multiple sequence alignment C_AF286232 LLEESQYQQERNEKDLLALDSWKNLWDWFNISNWLWYIK C_AF110975 LLEESQNQQEQNEKDLLALDSRNNLWSWFNISNWLWYIK C_U39239 LLEVSQNQQEENEKDLLALDKWQNLWSWFNISNWLWYIK C_AF286233 LLEVSQNQQEENEKDLLALDNWNILWSWFNITNWLWYIK C_AF286225 LLEVSQNQQENNERDLLALDS-KNLWNWFNITNWLWYIK C_U08454 LLEDSQNQQEKNEKDLLALDSWNNLWNWFNITKWLWYIK C_U08455 LLEDSQNQQERNEKDLLALDSWNNLWNWFNITNWLWYIK C_AJ276221 LLEESQNQQENNEKDLLALDSWKNLWSWFDITKWLWYIK C_AF067155 LLEESQNQQEENEKDLLALDSWKNLWNWFDITKWLWYIK C_AF067158 LLEDSQNQQEKNEKDLLALDSWKNLWSWFDITNWLWYIK C_AB023804 LLEESQNQQEKNEKDLLALDSWKNLWSWFDITNWLWYIK C_AF290028 LLEDSQNQQEKNEKDLLALDSWKNLWNWFGITNWLWYIK C_AF219274 LLEDSQNQQEKNEKDLLALDSWKNLWNWFSITNWLWYIK C_U08453 LLEDSQNQQEKNEKDLLALDSWKNLWNWFDITNWLWYIK C_AF110960 LLEESQTQQEKNEKDLLALDSWQNLWNWFSITNWLWYIK C_AF286231 LLEDSQTQQERNEKDLLALDNWKNLWNWFSITNWLWYIK C_U39257 LLEDSQNQQEKNEQELLALDKWQNLWNWFDISKWLWYIR C_AF286235 LLEDSQKQQEKNEQELLALDKWQNLWNWFSITKWLWYIK C_L22940 LLEDSQNQQEKNEQDLLALDKWQNLWNWFSITKWLWYIK C_U39238 LLEDSQNQQEKNEQDLLALDKWQNLWNWFDITKWLWYIK C_AF286228 LLEDSQNQQKKNEQDLLASDKWQNLWSWFDITKWLWYIK C_U09126 LLEDSQNQQEKNEQDLLALDKWQNLWTWFGITNWLWYIK C_U15121 LLEDSQNQQEKNEQDLLALDKWQNLWTWFGITNWLWYIK C_U39246 LLEVSQNPQEKNENDLLALDKWQNLWNWFSITKWLWYIK C_AF219262 LLEVSQNQQEKNEKDLLALDKWQNLWNWFGITKWLWYIK C_U39237 LLEESQNQQEKNEQDLLALEQWQNLWSWFSITNWLWYIR C_U39251 LLEESQNQQENNEKDLLALDKWQNLWSWFDITKWLWYIR C_AF286234 LLEESQTQQENNEKDLLALDKWNSLWTWFDITKWPWYIK C_U39243 LLEDSQTQQENNEKELLELDKWQNLWSWFDITNWLWYIK C_L23065 LLEVSQTQQEQNEKDLLALDKWQNLWSWFDITKWLWYIK *** ** *:.**.:** :. : ** **.*::* ***: Or, upload sequence 3. OPTIONS Logo Type Background amino acid distribution Type 1 Type 2 Equal Distribution (0.05) Custom: Enter amino acid probabilities pA pC pD pE pF pG pH pI pK pL pM pN pP pQ pR pS pT pV pW pY Server uses the DALILA package to create sequence logos from input files derived from sequence alignments using a perl script implemented by Pedro A. Reche. Perl script uses the method of J. Gorodkin et al. Comput. Appl. Biosci., Vol. 13, no. 6 pp 583-586, 1997 in which the standard sequence logo by Schneider and Stephens have been modify to take in consideration a priori amino acid distributions as well as gaps. When a priori aa probabilities are all set to 0.05 sequence logo is virtually identical to that described by Tom Schneiders Hits since June/2004 Last updated: This tool is also available at this site Contact Us    |   Immunomedicine Group    |