MPBind: A Meta-motif-based statistical framework and pipeline to Predict Binding potential of SELEX-derived aptamers

Bioinformatics

Volumn 30, Issue 18, 2014, Pages 2665-2667

  Jiang, Peng ^a   Meyer, Susanne ^a   Hou, Zhonggang ^a   Propson, Nicholas E ^a   Soh, H Tom ^a   Thomson, James A ^a,b   Stewart, Ron ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APTAMER; LIGAND; OLIGONUCLEOTIDE;

ARTICLE; BIOLOGY; COMBINATORIAL CHEMISTRY; COMPUTER PROGRAM; EMBRYONIC STEM CELL; ENZYME SPECIFICITY; HUMAN; METABOLISM; METHODOLOGY; SEQUENCE ANALYSIS;

APTAMERS, NUCLEOTIDE; COMPUTATIONAL BIOLOGY; EMBRYONIC STEM CELLS; HUMANS; LIGANDS; OLIGONUCLEOTIDES; SELEX APTAMER TECHNIQUE; SEQUENCE ANALYSIS; SOFTWARE; SUBSTRATE SPECIFICITY;

EID: 84907513604     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu348     Document Type: Article

References (9)

1. Cho, M. et al. (2010) Quantitative selection of DNA aptamers through microfluidic selection and high-throughput sequencing. Proc. Natl Acad. Sci. USA, 107, 15373-15378.
2. Daniels, D.A. et al. (2003) A tenascin-C aptamer identified by tumor cell SELEX: systematic evolution of ligands by exponential enrichment. Proc. Natl Acad. Sci. USA, 100, 15416-15421.
3. Dittmar, K.A. et al. (2012) Genome-wide determination of a broad ESRP-regulated posttranscriptional network by high-throughput sequencing. Mol. Cell. Biol., 32, 1468-1482.
4. Ng, E.W. et al. (2006) Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease. Nat. Rev. Drug Discov., 5, 123-132.
5. Sassanfar, M. and Szostak, J.W. (1993) An RNA motif that binds ATP. Nature, 364, 550-553.
6. Stouffer, S.A. et al. (1949) The American Soldier: Adjustment During Army Life (Studies in Social Psychology in World War II, Vol. 1.). Princeton University Press, Princeton, NJ.
7. Thiel, W.H. et al. (2012) Rapid identification of cell-specific, internalizing RNA aptamers with bioinformatics analyses of a cell-based aptamer selection. PloS One, 7, e43836.
8. Thiel, W.H. et al. (2011) Nucleotide bias observed with a short SELEX RNA apta-mer library. Nucleic Acid Ther., 21, 253-263.
9. Thomson, J.A. et al. (1998) Embryonic stem cell lines derived from human blasto-cysts. Science, 282, 1145-1147.