论文信息 - DNAFSMiner: a web-based software toolbox to recognize two types of functional sites in DNA sequences

DNAFSMiner: a web-based software toolbox to recognize two types of functional sites in DNA sequences

UNLABELLED DNAFSMiner (DNA Functional Sites Miner) is a web-based software toolbox to recognize functional sites in nucleic acid sequences. Currently in this toolbox, we provide two software: TIS Miner and Poly(A) Signal Miner. The TIS Miner can be used to predict translation initiation sites in vertebrate DNA/mRNA/cDNA sequences, and the Poly(A) Signal Miner can be used to predict polyadenylation [poly(A)] signals in human DNA sequences. The prediction results are better than those by literature methods on two benchmark applications. This good performance is mainly attributable to our unique learning method. DNAFSMiner is available free of charge for academic and non-profit organizations. AVAILABILITY http://research.i2r.a-star.edu.sg/DNAFSMiner/ CONTACT huiqing@i2r.a-star.edu.sg.

[1] Tetsuo Nishikawa,et al. Assessing protein coding region integrity in cDNA sequencing projects , 1998, Bioinform..

[2] Huiqing Liu,et al. An in-silico method for prediction of polyadenylation signals in human sequences. , 2003, Genome informatics. International Conference on Genome Informatics.

[3] Huiqing Liu,et al. Data Mining Tools for Biological Sequences , 2003, J. Bioinform. Comput. Biol..

[4] Jack E. Tabaska,et al. Detection of polyadenylation signals in human DNA sequences. , 1999, Gene.

[5] Artemis G. Hatzigeorgiou,et al. Translation initiation start prediction in human cDNAs with high accuracy , 2002, Bioinform..

[6] D. Gautheret,et al. Sequence determinants in human polyadenylation site selection , 2003, BMC Genomics.

[7] Anders Gorm Pedersen,et al. Neural Network Prediction of Translation Initiation Sites in Eukaryotes: Perspectives for EST and Genome Analysis , 1997, ISMB.

[8] Huiqing Liu,et al. Using amino acid patterns to accurately predict translation initiation sites , 2004, Silico Biol..

[9] M. Kozak. An analysis of 5'-noncoding sequences from 699 vertebrate messenger RNAs. , 1987, Nucleic acids research.