Sequence Bundles: A novel method for visualising, discovering and exploring sequence motifs

BMC Proceedings

Volumn 8, Issue , 2014, Pages

  Kultys, Marek ^a   Nicholas, Lydia ^a   Schwarz, Roland ^b   Goldman, Nick ^b   King, James ^a  

^a Science Practice   (United Kingdom)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; CONFERENCE PAPER; CONSENSUS SEQUENCE; CONSERVED SEQUENCE; DATA ANALYSIS SOFTWARE; GENE FUNCTION; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC CORRELATION; HUMAN; NONHUMAN; POSITION WEIGHT MATRIX; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; THICKNESS;

EID: 85018192794     PISSN: None     EISSN: 17536561     Source Type: Journal    
DOI: 10.1186/1753-6561-8-S2-S8     Document Type: Conference Paper

References (17)

1. Science Practice: Sequence Bundles. http://dx.doi.org/10.14435/sequence-bundles-biovis, [ http://science-practice.com/projects/sequence-bundles/ ]
2. Aniba MR, Poch O, Thompson JD: Issues in bioinformatics benchmarking: the case study of multiple sequence alignment. Nucleic Acids Research. 2010, 38 (21): 7353-7363. [ http://dx.doi.org/10.1093/nar/gkq625 ]
3. Kamena C, Notredame C: Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics. 2009, 25 (19): 2455-2465. [ http://dx.doi.org/10.1093/bioinformatics/btp452 ]
4. Schneider TD, Stephens RM: Sequence Logos: A New Way to Display Consensus Sequences. Nucleic Acids Research. 1990, 18 (20): 6097-6100. [ http://dx.doi.org/10.1093/nar/18.20.6097 ]
5. Schuster-Böckler B, Schultz J, Rahmann S: HMM Logos for visualization of protein families. BMC Bioinformatics. 2004, 5: 7-[ http://dx.doi.org/10.1186/14712105-5-7 ]
6. Thomsen MCF, Nielsen M: Seq2Logo: a method for construction and visualisation of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion. Nucleic Acids Research. 2012, 40: W281-W287. [ http://dx.doi.org/10.1093/nar/gks469 ]
7. Sharma V, Murphy DP, Provan G, Baranov PV: CodonLogo: a sequence logo-based viewer for codon patterns. Bioinformatics. 2012, 28 (14): 1935-1936. [ http://dx.doi.org/10.1093/bioinformatics/bts295 ]
8. O'Shea JP, Chou MF, Quader SA, Ryan JK, Church GM, Schwartz D: pLogo: a probabilistic approach to visualizing sequence motifs. Nature Methods. 2013, 10 (12): 1211-1212. [ http://dx.doi.org/10.1038/nmeth.2646 ]
9. Schwarz R, Seibel PN, Rahmann S, Schoen C, Huenerberg M, Müller-Reible C, Dandekar T, Karchin R, Schultz J, Müller T: Detecting species-site dependencies in large multiple sequence alignments. Nucleic Acid Research. 2009, 37 (18): 5959-5968.
10. International Institute for Information Design: idX (information design exchange) Information Design: Core Competencies, What information designers know and can do. 2007, International Institute for Information Design, Vienna, [ http://www.iiid.net/PDFs/idxPublication.pdf ]
11. 3rd IEEE Symposium on Biological Data Visualisation, BioVis 2013 Data Redesign Contest. [ http://biovis.net/year/2013/info/redesign-contest ]
12. Wampler JE: Tutorial on Peptide and Protein Structure. [ http://www.bmb.uga.edu/wampler/tutorial/ ]
13. Kultys M: Visual Alpha-Beta-Gamma: Rudiments of Visual Design for Data Explorers. Parsons Journal for Information Mapping. 2013, 5 (1): [ http://piim.newschool.edu/journal/issues/2013/01/index.php ]
14. Properties of Amino Acids. Handbook of Chemistry and Physics, Internet Version 2005. Edited by: Lide DR. 2005, Boca Raton FL: CRC Press
15. Processing 2. [ http://processing.org ]
16. Ward M, Grinstein G, Keim D: Interactive Data Visualisation. 2010, Natick MA: A K Peters
17. Becker RA, Cleveland WS: Brushing Scatterplots. Technometrics. 1987, 29 (2): 127-142. [ http://dx.doi.org/10.1080/00401706.1987.10488204 ]