SnipViz: A compact and lightweight web site widget for display and dissemination of multiple versions of gene and protein sequences

BMC Research Notes

Volumn 7, Issue 1, 2014, Pages

  Jaschob, Daniel ^a   Davis, Trisha N ^a   Riffle, Michael ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SACCHAROMYCES CEREVISIAE PROTEIN;

AMINO ACID SEQUENCE; CHEMISTRY; COMPUTER INTERFACE; COMPUTER PROGRAM; FUNGAL GENE; GENETICS; HUMAN; INTERNET; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROCEDURES; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; BASE SEQUENCE; GENES, FUNGAL; HUMANS; INTERNET; MOLECULAR SEQUENCE DATA; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE ANALYSIS; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 84904526860     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-7-468     Document Type: Article

References (11)

1. Improved tools for biological sequence comparison. Pearson WR, Lipman DJ, Proc Natl Acad Sci U S A 1988 85 8 2444 2448 10.1073/pnas.85.8.2444 3162770
2. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Thompson JD, Higgins DG, Gibson TJ, Nucleic Acids Res 1994 22 22 4673 4680 10.1093/nar/22.22.4673 7984417 (Pubitemid 24354800)
3. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Soding J, Thompson JD, Higgins DG, Mol Syst Biol 2011 7 539 21988835
4. Clustal W and Clustal X version 2.0. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG, Bioinformatics 2007 23 21 2947 2948 10.1093/bioinformatics/btm404 17846036 (Pubitemid 350162903)
5. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Katoh K, Standley DM, Mol Biol Evol 2013 30 4 772 780 10.1093/molbev/mst010 23329690
6. MView: a web-compatible database search or multiple alignment viewer. Brown NP, Leroy C, Sander C, Bioinformatics 1998 14 4 380 381 10.1093/bioinformatics/14.4.380 9632837 (Pubitemid 28393806)
7. Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ, Bioinformatics 2009 25 9 1189 1191 10.1093/bioinformatics/btp033 19151095
8. T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. Di Tommaso P, Moretti S, Xenarios I, Orobitg M, Montanyola A, Chang JM, Taly JF, Notredame C, Web Server issue, Nucleic Acids Res 2011 39 13 W17 10.1093/nar/gkr245 21558174
9. The Newick tree format. http://evolution.genetics.washington.edu/phylip/ newicktree.html
10. Amino acid substitution matrices from protein blocks. Henikoff S, Henikoff JG, Proc Natl Acad Sci U S A 1992 89 22 10915 10919 10.1073/pnas.89.22.10915 1438297
11. Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast. Skelly DA, Merrihew GE, Riffle M, Connelly CF, Kerr EO, Johansson M, Jaschob D, Graczyk B, Shulman NJ, Wakefield J, Cooper SJ, Fields S, Noble WS, Muller EG, Davis TN, Dunham MJ, Maccoss MJ, Akey JM, Genome Res 2013 23 9 1496 1504 10.1101/gr.155762.113 23720455