WebLogo: a sequence logo generator.

WebLogo generates sequence logos, graphical representations of the patterns within a multiple sequence alignment. Sequence logos provide a richer and more precise description of sequence similarity than consensus sequences and can rapidly reveal significant features of the alignment otherwise difficult to perceive. Each logo consists of stacks of letters, one stack for each position in the sequence. The overall height of each stack indicates the sequence conservation at that position (measured in bits), whereas the height of symbols within the stack reflects the relative frequency of the corresponding amino or nucleic acid at that position. WebLogo has been enhanced recently with additional features and options, to provide a convenient and highly configurable sequence logo generator. A command line interface and the complete, open WebLogo source code are available for local installation and customization.

[1]  N. Seeman,et al.  Sequence-specific Recognition of Double Helical Nucleic Acids by Proteins (base Pairs/hydrogen Bonding/recognition Fidelity/ion Binding) , 2022 .

[2]  T. D. Schneider,et al.  A design for computer nucleic-acid-sequence storage, retrieval, and manipulation. , 1982, Nucleic acids research.

[3]  T. D. Schneider,et al.  Information content of binding sites on nucleotide sequences. , 1986, Journal of molecular biology.

[4]  D. Higgins,et al.  See Blockindiscussions, Blockinstats, Blockinand Blockinauthor Blockinprofiles Blockinfor Blockinthis Blockinpublication Clustal: Blockina Blockinpackage Blockinfor Blockinperforming Multiple Blockinsequence Blockinalignment Blockinon Blockina Minicomputer Article Blockin Blockinin Blockin , 2022 .

[5]  D. Lipman,et al.  Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[6]  B. Matthews,et al.  Structural basis of DNA-protein recognition. , 1989, Trends in biochemical sciences.

[7]  T. D. Schneider,et al.  Sequence logos: a new way to display consensus sequences. , 1990, Nucleic acids research.

[8]  T. Steitz,et al.  Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees , 1991, Science.

[9]  Thomas M. Cover,et al.  Elements of Information Theory , 2005 .

[10]  T. D. Schneider,et al.  Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites. , 1992, Journal of molecular biology.

[11]  M. C. Shaner,et al.  Sequence logos: a powerful, yet simple, tool , 1993, [1993] Proceedings of the Twenty-sixth Hawaii International Conference on System Sciences.

[12]  A. Stewart.  Genes V , 1994 .

[13]  S. Henikoff,et al.  Automated construction and graphical presentation of protein blocks from unaligned sequences. , 1995, Gene.

[14]  Gary Parkinson,et al.  Aromatic hydrogen bond in sequence-specific protein DNA recognition , 1996, Nature Structural Biology.

[15]  Gary D. Stormo,et al.  Displaying the information contents of structural RNA alignments: the structure logos , 1997, Comput. Appl. Biosci..

[16]  T. D. Schneider,et al.  Information content of individual genetic sequences. , 1997, Journal of theoretical biology.

[17]  G. Stormo.  Information content and free energy in DNA--protein interactions. , 1998, Journal of theoretical biology.

[18]  G. Church,et al.  A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. , 1998, Journal of molecular biology.

[19]  T. D. Schneider,et al.  The human XPG gene: gene architecture, alternative splicing and single nucleotide polymorphisms. , 2001, Nucleic acids research.

[20]  T. D. Schneider,et al.  Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation. , 2001, Nucleic acids research.

[21]  Michael Y. Galperin,et al.  Novel domains of the prokaryotic two-component signal transduction systems. , 2001, FEMS microbiology letters.

[22]  Biaoyang Lin,et al.  The program of androgen-responsive genes in neoplastic prostate epithelium , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Michael Y. Galperin,et al.  An extracellular calcium-binding domain in bacteria with a distant relationship to EF-hands. , 2003, FEMS microbiology letters.