JUICE: A data management system that facilitates the analysis of large volumes of information in an EST project workflow

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Latorre, Mariano ^a,b   Silva, Herman ^a,b   Saba, Juan ^a,b   Guziolowski, Carito ^a,b   Vizoso, Paula ^a,b   Martinez, Veronica ^a,b   Maldonado, Jonathan ^a,b   Morales, Andrea ^a,b   Caroca, Rodrigo ^a,b   Cambiazo, Veronica ^b   Campos Vargas, Reinaldo ^c   Gonzalez, Mauricio ^b   Orellana, Ariel ^a,b   Retamales, Julio ^b,c,d   Meisel, Lee A ^a,b  

^a UNIVERSIDAD ANDRÉS BELLO   (Chile)

^b UNIVERSITY OF CHILE   (Chile)

^c INSTITUTO DE INVESTIGACIONES AGROPECUARIAS   (Chile)

^d Valent BioSciences Corporation   (Chile)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL PROCESS; CANDIDATE GENES; DATA MANAGEMENT SYSTEM; EXPRESSED SEQUENCE TAGS; FUNCTIONAL GENOMICS; GENERAL PUBLIC LICENSE; OPEN SOURCE DATUM; SEQUENCE INFORMATIONS;

COMPUTER OPERATING SYSTEMS; INFORMATION MANAGEMENT; PIPELINES;

OPEN SYSTEMS;

ACCESS TO INFORMATION; ARTICLE; BIOINFORMATICS; COMPUTER ANALYSIS; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER PROGRAM; EXPRESSED SEQUENCE TAG; FUNCTIONAL GENOMICS; GENE SEQUENCE; INFORMATION RETRIEVAL; PROCESS DEVELOPMENT; SYSTEMS BIOLOGY; WEB BROWSER; BIOLOGY; CHROMATOGRAPHY; COMPUTER LANGUAGE; DATA BASE; DNA SEQUENCE; GENETIC DATABASE; GENOME; GENOMICS; INFORMATION SYSTEM; NUCLEIC ACID DATABASE; PROCEDURES;

CHROMATOGRAPHY; COMPUTATIONAL BIOLOGY; DATABASE MANAGEMENT SYSTEMS; DATABASES, GENETIC; DATABASES, NUCLEIC ACID; EXPRESSED SEQUENCE TAGS; GENOME; GENOMICS; MANAGEMENT INFORMATION SYSTEMS; PROGRAMMING LANGUAGES; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 33845270203     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-513     Document Type: Article

References (48)

1. International Rice Genome Sequencing Project: The map-based sequence of the rice genome. Nature 2005, 436:793-800.
2. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, et al. The Sequence of the Human Genome. Science 2001, 291:1304-1351.
3. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, Sutton GG, Wortman JR, Yandell MD, Zhang Q, Chen LX, Brandon RC, Rogers YH, Blazej RG, Champe M, Pfeiffer BD, Wan KH, Doyle C, Baxter EG, Helt G, Nelson CR, Gabor GL, Abril JF, Agbayani A, An HJ, Andrews-Pfannkoch C, Baldwin D, Ballew RM, Basu A, Baxendale J, Bayraktaroglu L, Beasley EM, Beeson KY, Benos PV, Berman BP, Bhandari D, Bolshakov S, Borkova D, Botchan MR, Bouck J, Brokstein P, Brottier P, Burtis KC, Busam DA, Butler H, Cadieu E, Center A, Chandra I, Cherry JM, Cawley S, Dahlke C, Davenport LB, Davies P, de Pablos B, Delcher A, Deng Z, Mays AD, Dew I, Dietz SM, Dodson K, Doup LE, Downes M, Dugan-Rocha S, Dunkov BC, Dunn P, Durbin KJ, Evangelista CC, Ferraz C, Ferriera S, Fleischmann W, Fosler C, Gabrielian AE, Garg NS, Gelbart WM, Glasser K, Gloclek A, Gong F, Gorrell JH, Gu Z, Guan P, Harris M, Harris NL, Harvey D, Heiman TJ, Hernandez JR, Houck J, Hostin D, Houston KA, Howland TJ, Wei MH, et al. The Genome Sequence of Drosophila melanogaster. Science 2000, 287:2185-2195.
4. The Arabidopsis Genome Initiative: Analysis of the genome sequence of the flowering plant Arobidopsis thaliana. Nature 2000, 408:796-815.
5. Whitfield CW, Band MR, Ronaldo MF, Kumar CG, Liu L, Pardinas JR, Robertson HM, Soares MB, Robinson GE: Annotated Expressed Sequence Tags and cDNA Microarrays for Studies of Brain and Behavior in the Honey Bee. Gename Res 2002, 12:555-566.
6. Hecht J, Kuhl H, Haas SA, Bauer S, Poustka AJ, Lienau J, Schell H, Stiege AC, Seitz V, Reinhardt R, Duda GN, Mundlos S, Robinson PN: Gene identification and analysis of transcripts differentially regulated in fracture healing by EST sequencing in the domestic sheep. BMC Genomics 2006, 7:172.
7. Carre W, Wang X, Porter TE, Nys Y, Tang J, Bernberg E, Morgan R, Burnside J, Aggrey SE, Simon J, Cogburn LA: Chicken genomics resource: sequencing and annotation of 35,407 ESTs from single and multiple tissue cDNA libraries and CAP3 assembly of a chicken gene index. Physiol Genomics 2006, 25:514-24.
8. Ramirez M, Graham MA, Blanco-Lopez L, Silvente S, Medrano-Soto A, Blair MW, Hernandez G, Vance CP, Lara M: Sequencing and analysis of common bean ESTs. Building a foundation for functional genomics. Plant Physiol 2005, 137:1211-27.
9. Fernandez P, Paniego N, Lew S, Hopp HE, Heinz RA: Differential representation of sunflower ESTs in enriched organ-specific cDNA libraries in a small scale sequencing project. BMC Genomics 2003, 4:40-48.
10. Bono H, Yagi K, Kasukawa T, Nikaido I, Tominaga N, Miki R, Mizuno Y, Tomaru Y, Goto H, Nitanda H, Shimizu D, Makino H, Morita T, Fujiyama J, Sakai T, Shimoji T, Hume DA, Hayashizaki Y, Okazaki Y, RIKEN GER Group; GSL Members: Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays. Genome Res 2003, 13 (6B): 1318-23.
11. Zhang H, Sreenivasulu N, Weschke W, Stein N, Rudd S, Radchuk V, Potokina E, Scholz U, Schweizer P, Zierold U, Langridge P, Varshney RK, Wobus U, Graner A: Large-scale analysis of the barley transcriptome based on expressed sequence tags. The Plant Journal 2004, 40:276-290.
12. Vizcaino JA, Gonzalez FJ, Suarez MB, Redondo J, Heinrich J, Delgado-Jarana J, Hermosa R, Gutierrez S, Monte E, Llobell A, Rey M: Generation, annotation and analysis of ESTs from Trichoderma harzianum CECT 2413. BMC Genomics 2006, 7:193.
13. Yu JK, Sun Q, Rota ML, Edwards H, Telera H, Sorrells ME: Expressed sequence tag analysis in tef (Eragrostis tef (Zucc) Trotter). Genome 2006, 49:365-72.
14. Lin C, Mueller LA, Mc Carthy J, Crouzillat D, Petiard V, Tanksley SD: Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts. Theor Appl Genet 2005, 112:114-30.
15. Ewing B, Hillier L, Wendl MC, Green P: Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment. Genome Res 1998, 8:175-185.
16. Ewing B, Green P: Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998, 8:186-94.
17. Gordon D, Abajian C, Green P, Consed: a graphical tool for sequence finishing. Genome Res 1998, 8:195-202.
18. Huang X, Madan A: CAP3: A DNA sequence assembly program. Genome Res 1999, 9:868-77.
19. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
20. Zdobnov EM, Apweiler R: InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics 2001, 17:847-848.
21. Paquola AC, Nishyiama MY Jr, Reis EM, Da Silva AM, Verjovski-Almeida S: ESTWeb: bioinformatics services for EST sequencing projects. Bioinformatics 2003, 19:1587-1588.
22. Kumar CG, LeDuc R, Gong G, Roinishivili L, Lewin HA, Liu L: ESTIMA, a tool for EST management in a multi-project environment. BMC Bioinformatics 2004, 5:176-185.
23. Christoffels A, Van Gelder A, Greyling G, Miller R, Hide T, Hide W: STACK: Sequence Tag Alignment and Consensus Knowledgebase. Nucleic Acids Res 2001, 29:234-238.
24. Mao C, Cushman JC, May GD, Weller JW: ESTAP - An automated system for the analysis of EST data. Bioinformatics 2003, 19:1720-1722.
25. Ayoubi P, Jin X, Leite S, Liu X, Martajaja J, Abduraham A, Wan Q, Yan W, Misawa E, Prade RA: PipeOnline 2.0 automated EST processing and functional data sorting. Nucleic Acids Res 2002, 30:4761-4769.
26. Okubo K, Hori N, Matoba R, Niiyama T, Fukushima A, Kojima Y, Matsubara K: Large scale cDNA sequencing for analysis of quantitative and qualitative aspects of gene expression. Nature Genetics 1992, 2:173-179.
27. Liang F, Holt I, Pertea G, Karamycheva S, Salzberg S, Quackenbush J: An optimized protocol for analysis of EST sequences. Nucleic Acids Res 2000, 28:3657-3665.
28. Rounsley S, Glodek A, Sutton G, Adams M, Somerville C, Venter J, Kerlavage A: The construction of Arabidopsis Expressed Sequence Tag Assemblies. Plant Physiology 1996, 112:1177-1183.
29. Lee WH, Vega VB: Heterogeneity detector: finding heterogeneous positions in Phred/Phrap assemblies. Bioinformatics 2004, 20(16):2863-4.
30. Kim H, Schmidt CJ, Decker KS, Emara MG: A double-screening method to identify reliable candidate non-synonymous SNPs from chicken EST data. Anim Genet 2003, 34:249-54.
31. Lee SH, Park EW, Cho YM, Lee JW, Kim HY, Lee JH, Oh SJ, Cheong IC, Yoon DH: Confirming single nucleotide polymorphisms from expressed sequence tag datasets derived from three cattle cDNA libraries. J Biochem Mol Biol 2006, 39:183-188.
32. Cheng TC, Xia QY, Qian JF, Liu C, Lin Y, Zha XF, Xiang ZH: Mining single nucleotide polymorphisms from EST data of silkworm, Bombyx mori, inbred strain Dazao. Insect Biochem Mol Biol 2004, 34:523-530.
33. Huang Y, Pumphrey J, Gingle AR: ESTminer: a Web interface for mining EST contig and cluster databases. Bioinformatics 2005, 21:669-70.
34. Parkinson J, Anthony A, Wasmuth J, Schmid R, Hedley A, Blaxter M: PartiGene - constructing partial genomes. Bioinformatics 2004, 20:1398-404.
35. Matukumalli LK, Grefenstette JJ, Sonstegard TS, Van Tassell CP: ESTPAGE - managing and analyzing EST data. Bioinformatics 2004, 20:286-288.
36. Hotz-Wagenblatt A, Hankeln T, Ernst P, Glatting KH, Schmidt ER, Suhai S: ESTAnnotator: A tool for high throughput EST annotation. Nucleic Acids Res 2003, 31:3716-3719.
37. Xu H, He L, Zhu Y, Huang W, Fang L, Tao L, Zhu Y, Cai L, Xu H, Zhang L, Xu H, Zhou Y: EST pipeline system: detailed and automated EST data processing and mining. Genomics Proteomics Bioinformatics 2003, 1(3):236-42.
38. Meisel L, Fonseca B, Gonzalez S, Baeza-Yates R, Cambiazo V, Campos R, Gonzalez M, Orellana A, Retamales J, Silva H: A rapid and efficient method for purifying high quality total RNA from peaches (Prunus persica) for functional genomics analyses. Biol Res 2005, 38(1):83-88.
39. Campos-Vargas R, Becerra O, Baeza-Yates R, Cambiazo, V, Gonzalez M, Meisel L, Orellana A, Retamales J, Silva H, Defilippi BG: Seasonal variation in the development of chilling injury in 'O'Henry' peaches. Scientia Horticulturae 2006, 110:79-83.
40. Meisel L: The Chilean Gene Hunt, A functional genomics approach towards identifying candidate genes associated with peach/nectarine fruit quality. Summerfruit Australia Quarterly 2006, 8:17.
41. Vector Masking [http://www.ncbi.nlm.nih.gov/VecScreen/VecScreen.html]
42. TrimmerX [http://www.genomavegetal.cl/]
43. Telles G, Silva F: Trimming and clustering sugarcane ESTs. Genetics and Molecular Biology 2001, 24:17-23.
44. FASTA [http://workshop.molecularevolution.org/resources/fileformats/]
45. PHP [http://www.php.net/]
46. MySQL [http://www.mysql.com/]
47. Chromatogram Applet, Release I, 6/30/96 by Eugen Buehler.. snafuτelerama.lm.com
48. Durham AM, Kashiwabara AY, Matsunaga TG, Ahagon PH, Rainone F, Varuzza L, Gruber A: EGene: a configurable pipeline generation system for automated sequence analysis. Bioinformatics 2005, 21:2812-2813.