WebLogo

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.


References in zbMATH (referenced in 24 articles )

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  1. Giancarlo, Raffaele; Rombo, Simona E.; Utro, Filippo: DNA combinatorial messages and epigenomics: the case of chromatin organization and nucleosome occupancy in eukaryotic genomes (2019)
  2. Ju, Zhe; Cao, Jun-Zhe; Gu, Hong: iLM-2L: a two-level predictor for identifying protein lysine methylation sites and their methylation degrees by incorporating K-gap amino acid pairs into Chou’s general PseAAC (2015)
  3. Shreif, Zeina; Striegel, Deborah A.; Periwal, Vipul: The jigsaw puzzle of sequence phenotype inference: piecing together Shannon entropy, importance sampling, and empirical Bayes (2015)
  4. González-Álvarez, David L.; Vega-Rodríguez, Miguel A.; Rubio-Largo, Álvaro: Convergence analysis of some multiobjective evolutionary algorithms when discovering motifs (2014) ioport
  5. Kasabov, Nikola (ed.): Springer handbook of bio-/neuro-informatics (2014)
  6. Hwa, Kuo-Yuan; Subramani, Boopathi; Khoo, Kay-Hooi: Putative xylosyltransferase genes in trichomonas vaginalis (2012) ioport
  7. Shi, Shao-Ping; Qiu, Jian-Ding; Sun, Xing-Yu; Suo, Sheng-Bao; Huang, Shu-Yun; Liang, Ru-Ping: A method to distinguish between lysine acetylation and lysine methylation from protein sequences (2012)
  8. Tavares, Raphael; Renaud, Gabriel; Oliveira, Paulo Sergio Lopes; Ferreira, Carlos G.; Dias-Neto, Emmanuel; Passetti, Fabio: Identical sequence patterns in the ends of exons and introns of human protein-coding genes (2012)
  9. de Avila e Silva, Scheila; Echeverrigaray, Sergio; Gerhardt, Günther J. L.: BacPP: bacterial promoter prediction -- a tool for accurate sigma-factor specific assignment in enterobacteria (2011)
  10. Giraud, Mathieu; Varré, Jean-Stéphane: Parallel position weight matrices algorithms (2011) ioport
  11. Knapp, Bernhard; Giczi, Verena; Ribarics, Reiner; Schreiner, Wolfgang: Peptx: using genetic algorithms to optimize peptides for MHC binding (2011) ioport
  12. Erill, Ivan; O’neill, Michael C.: A reexamination of information theory-based methods for DNA-binding site identification (2009) ioport
  13. Gowrisankar, Sivakumar; Jegga, Anil G.: Regression based predictor for p53 transactivation (2009) ioport
  14. Paul Murrell: Importing Vector Graphics: The grImport Package for R (2009) not zbMATH
  15. Janky, Rekin’s; Van Helden, Jacques: Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution (2008) ioport
  16. Kim, Hyeoncheol; Zhang, Yiying; Heo, Yong-Seok; Oh, Heung-Bum; Chen, Su-Shing: Specificity rule discovery in HIV-1 protease cleavage site analysis (2008)
  17. Dogan, Rezarta Islamaj; Getoor, Lise; Wilbur, W. John; Mount, Stephen M.: Features generated for computational splice-site prediction correspond to functional elements (2007) ioport
  18. Feng, Xiucheng; Wan, Lin; Deng, Minghua; Sun, Fengzhu; Qian, Minping: An efficient algorithm for deciphering regulatory motifs (2007)
  19. Inouchi, Atsushi; Shinohara, Shuichi; Inoue, Hiroshi; Kita, Kenji; Itakura, Mitsuo: Identification of specific sequence motifs in the upstream region of 242 human miRNA genes (2007)
  20. Redhead, Emma; Bailey, Timothy L.: Discriminative motif discovery in DNA and protein sequences using the DEME algorithm (2007) ioport

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