Integrating human genome database into electronic health record with sequence alignment and compression mechanism

Journal of Medical Systems

Volumn 36, Issue 4, 2012, Pages 2587-2597

  Chen, Wei Hsin ^a   Lu, Yu Wen ^a   Lai, Feipei ^a   Chien, Yin Hsiu ^b   Hwu, Wuh Liang ^b  

^a NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^b NATIONAL TAIWAN UNIVERSITY HOSPITAL   (Taiwan)

Author keywords

DNA sequencing; Health Information System; Human genome database system; Sequence alignment; Sequence compression; System integration; Web based database

Indexed keywords

ALGORITHM; ARTICLE; BASE MISPAIRING; BIOINFORMATICS; DNA COMPRESSION ALGORITHM; DNA SEQUENCE; ELECTRONIC MEDICAL RECORD; GENE DELETION; GENE INSERTION; GENOMICS; HEALTH CARE PLANNING; HEALTH CARE SYSTEM; HUMAN; HUMAN GENOME DATABASE SYSTEM; MEDICAL INFORMATION SYSTEM; MEGA BLAST ALGORITHM; COMPUTER PROGRAM; COMPUTER SYSTEM; GENETIC DATABASE; HUMAN GENOME; INFORMATION PROCESSING; INTERNET; NUCLEIC ACID DATABASE; SYSTEM ANALYSIS;

ALGORITHMS; COMPUTER SYSTEMS; DATA COMPRESSION; DATABASES, GENETIC; DATABASES, NUCLEIC ACID; ELECTRONIC HEALTH RECORDS; GENOME, HUMAN; HUMANS; INTERNET; SOFTWARE DESIGN; SYSTEMS INTEGRATION;

EID: 84873027492     PISSN: 01485598     EISSN: 1573689X     Source Type: Journal    
DOI: 10.1007/s10916-011-9731-0     Document Type: Article

References (28)

1. Blastall. http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastall/.
2. DNA sequencing. http://genomics.org/index.php/DNA-sequencing.
3. Sanger, F., Air, G. M., Barrell, B. G., Brown, N. L., Coulson, A. R., Fiddes, C. A., Hutchison, C. A., Slocombe, P. M., and Smith, M., Nucleotide sequence of bacteriophage phi X174 DNA. Nature 265(5596):687-695, 1977.
4. Shendure, J., and Ji, H., Next-generation DNA sequencing. Nat. Biotechnol. 26(10):1135-1145, 2008.
5. Human Genome Project HomePage. http://hgph.com/index.htm.
6. Human Genome Project Information. http://www.ornl.gov/sci/techresources/ Human-Genome/home.shtml.
7. McGinnis, S., and Madden, T. L., BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res. 32:20-25, 2004.
8. Benson, D. A., Boguski, M. S., Lipman, D. J., Ostell, J., Ouellette, B. F., Rapp, B. A., and Wheeler, D. L., GenBank. Nucleic Acids Res. 27(1):12-17, 1999.
9. Hubbard, T., Barker, D., Birney, E., Cameron, G., Chen, Y., Clark, L., Cox, T., Cuff, J., Curwen, V., Down, T., Durbin, R., Eyras, E., Gilbert, J., Hammond, M., Huminiecki, L., Kasprzyk, A., Lehvaslaiho, H., Lijnzaad, P., Melsopp, C., Mongin, E., Pettett, R., Pococok, M., Potter, S., Rust, A., Schmidt, E., Searles, S., Slater, G., Smith, J., Spooner, W., Stabenau, A., Stalker, J., Stupka, E., Ureta-Vidal, A., Vastrk, I., and Clamp, M., The Ensembl genome database project. Nucleic Acids Res. 30(1):38-41, 2002.
10. Tateno, Y., Miyazaki, S., Ota, M., Sugawara, M., and Gojobori, T., DNA Data Bank of Japan (DDBJ) in collaboration with mass sequencing teams. Nucleic Acids Res. 28(1):24-26, 2000.
11. Blake, J. A., Richardson, J. E., Bult, C. J., Kadin, J. A., and Eppig, J. P., MGD: the Mouse Genome Database. Nucleic Acids Res. 31(1):193-195, 2003.
12. Maruyama, Y., Wakamatsu, A., Kawamura, Y., Kimura, K., Yamamoto, J., Nishikawa, T., Kisu, Y., Sugano, S., Goshima, N., Isogai, T., and Nomura, N., Human Gene and Protein Database (HGPD): a novel database presenting a large quantity of experiment-based results in human proteomics. Nucleic Acids Res. 37:762-766, 2009.
13. Pruitt, K. D., Tatusova, T., and Maglott, D. R., NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35:61-65, 2006.
14. NCBI Reference Sequence (RefSeq). http://www.ncbi.nlm.nih.gov/RefSeq/.
15. BLAST Program Selection Guide. http://blast.ncbi.nlm.nih.gov/blast/ producttable.shtml.
16. MegaBLAST Search. http://www.ncbi.nlm.nih.gov/blast/megablast.shtml.
17. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipmen, D. J., Basic local alignment search tool. J. Mol. Biol. 215(3):403-410, 1990.
18. Grumbach, S. and Tahi, F., Compression of DNA sequences. Data Compression Conference. (pp. 340-350). IEEE Computer Society Press, 1993.
19. Chen, X., Kwong, S., and Li, M., A compression algorithm for DNA sequences and its applications in genome comparison. The 10th Workshop on Genome Informatics. (pp. 51-61). Genome Informatics Press, 1999
20. Chen, X., Li, M., Ma, B., and Tromp, J., DNACompress: fast and effective DNA sequence compression. Bioinformatics 18(12):1696-1698, 2002.
21. Ma, B., Tromp, J., and Li, M., PatternHunter: faster and more sensitive homology search. Bioinformatics 18(3):440-445, 2002.
22. Behzadi, B., and Fessant, F. L., DNA compression challenge revisited: a dynamic programming approach. Lect. Notes Comput. Sci. 3537:190-200, 2005.
23. Jurka, J., Kapitonov, V. V., Pavlice, A., Klonowski, P., Kohany, O., and Walichiewicz, J., Repbase update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110(1-4):462-467, 2005.
24. FASTA format description. http://www.ncbi.nlm.nih.gov/blast/fasta.shtml.
25. Apostolico, A., and Fraenkel, A., Robust transmission of unbounded strings using Fibonacci representations. IEEE Trans. Inf. Theory 33(2):238-245, 1987.
26. Elias, P., Universal codeword sets and representations of the integers. IEEE Trans. Inf. Theory 21(2):194-203, 1975.
27. Li, R., Li, Y., Kristiansen, K., and Wang, J., SOAP: short oligonucleotide alignment program. Bioinformatics 24(5):713-714, 2008.
28. Genetic Information Nondiscrimination Act of 2008 (Public Law 110-233).