MAGIC-SSP: A database-driven DNA sequence processing package with associated management tools

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Liang, Chun ^a,d   Sun, Feng ^a,e   Wang, Haiming ^a,f   Qu, Junfeng ^b   Freeman Jr , Robert M ^c   Pratt, Lee H ^a   Cordonnier Pratt, Marie Michèle ^a  

^a UNIVERSITY OF GEORGIA   (United States)

^b Harvard Medical School ^*  (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

^d MIAMI UNIVERSITY   (United States)

^e Nanosphere Inc   (United States)

^f NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DATA REPOSITORIES; DNA SEQUENCE DATA; IMPROVE PERFORMANCE; JAVA GRAPHICAL USER INTERFACE; LABORATORY INFORMATION MANAGEMENT SYSTEM; MULTIPLE PROJECTS; RELATIONAL DATABASE; RESEARCH PROGRAMS;

DATABASE SYSTEMS; DNA SEQUENCES; INFORMATION MANAGEMENT;

PIPELINE PROCESSING SYSTEMS;

ALGORITHM; ARTICLE; AUTOMATION; COMPUTER INTERFACE; DATA BASE; DNA SEQUENCE; ERROR; INFORMATION PROCESSING; INFORMATION SYSTEM; MONITORING; QUALITY CONTROL; COMPUTER GRAPHICS; COMPUTER LANGUAGE; DATABASE MANAGEMENT SYSTEM; EVALUATION STUDY; INFORMATION RETRIEVAL; NUCLEIC ACID DATABASE; PROCEDURES; SEQUENCE ALIGNMENT; SOFTWARE;

ALGORITHMS; COMPUTER GRAPHICS; DATABASE MANAGEMENT SYSTEMS; DATABASES, NUCLEIC ACID; INFORMATION STORAGE AND RETRIEVAL; PROGRAMMING LANGUAGES; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 33645467566     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-115     Document Type: Article

References (29)

1. Cordonnier-Pratt M-M, Liang C, Wang H, Kolychev D, Sun F, Freeman R, Sullivan R, Pratt LH: MAGIC Database and interfaces: an integrated package for gene discovery and expression. Comp Funct Genom 2004, 5:268-275.
2. Chou H-H, Holmes MH: DNA sequence quality trimming and vector removal. Bioinformatics 2001, 17:1093-1104.
3. Qiu F, Guo L, Wen T-J, Liu F, Ashlock DA, Schnable PS: DNA sequence-based "Bar codes" for tracking the origins of expressed sequence tags from a maize cDNA library constructed using multiple mRNA sources. Plant Physiol 2003, 133:475-481.
4. Sorek R, Safer HM: A novel algorithm for computational identification of contaminated EST libraries. Nucleic Acids Res 2003, 31:1067-1074.
5. Venter JC, Levy S, Stockwell T, Remington K, Halpern A: Massive parallelism, randomness and genomic advances. Nature Genetics 2003, 33:219-227.
6. Scheetz TE, Trivedi N, Roberts CA, Kucaba T, Berger B, Robinson NL, Birkett CL, Gavin AJ, O'Leary B, Braun TA, Bonaldo MF, Robinson JP, Sheffield VC, Soares MB, Casavant TL: ESTprep: preprocessing cDNA sequence reads. Bioinformatics 2003, 19:1318-1324.
7. Staden R: The Staden sequence analysis package. Mol Biotechnol 1996, 5:233-241.
8. Veklerov E, Eeckman FH, Martin CH: MTT: a software tool for quality control in sequence assembly. Microb Comp Genomics 1996, 1:179-184.
9. Smith TM, Abajian C, Hood L: Hopper: software for automating data tracking and flow in DNA sequencing. Comput Appl Biosci 1997, 13:175-82.
10. Wendl MC, Dear S, Hodgson D, Hillier L: Automated sequence preprocessing in a large-scale sequencing environment. Genome Res 1998, 8:975-984.
11. Inman JT, Flores HR, May GD, Weller JW, Bell CJ: A high-throughput distributed DNA sequence analysis and database system. IBM SYSTEMS JOURNAL 2001, 40:464-486.
12. 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.
13. Parkinson J, Anthony A, Wasmuth J, Schmid R, Hedley A, Blaxter M: PartiGene - constructing partial genomes. Bioinformatics 2004, 20:1398-1404.
14. Mao C, Cushman JC, May GD, Weller JW: ESTAP - an automated system for the analysis of EST data. Bioinformatics 2003, 19:1720-1722.
15. Paquola ACM, Nishyiama MY Jr, Reis EM, da Silva AM, Verjovski-Almeida S: ESTWeb: bioinformatics services for EST sequencing projects. Bioinformatics 2003, 19:1587-1588.
16. MAGIC SeqView [http://fungen.org/seqview]
17. Chen PP: The entity-relationship model - toward a unified view of data. ACM Transactions on Database Systems 1976, 1:9-36.
18. Favre L: UML and the unified process Hershey, PA, IRM Press; 2003.
19. 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.
20. CROSS_MATCH [http://Bozeman.mbt.washington.edu/phrap.docs/phrap.html]
21. Ning Z, Cox AJ, Mullikin JC: SSAHA: A Fast Search Method for Large DNA Databases. Genome Res 2001, 11:1725-1729.
22. MAGIC DB [http://fungen.org]
23. Weems D, Miller N, Garcia-Hernandez M, Huala E, Rhee SY: Design, implementation and maintenance of a model organism database for Arabidopsis thaliana. Comp Funct Genom 2004, 5:362-369.
24. Shah SP, He DYM, Sawkins JN, Druce JC, Quon G, Lett D, Zheng GXY, Xu T, Ouellette BFF: Pegasys: software for executing and integrating analyses of biological sequences. BMC Bioinformatics 2004, 5:40.
25. Potter SC, Clarke L, Curwen V, Keenan S, Mongin E, Searle SMJ, Stabenau A, Storey R, Clamp M: The Ensembl Analysis Pipeline. Genome Res 2004, 14:934-941.
26. Hoon H, Ratnapu KK, Chia J-M, Kumarasamy B, Xiao J, Clamp M, Stabenau A, Potter S, Clarke L, Stupka E: Biopipe: A Flexible Framework for Protocol-Based Bioinformatics Analysis. Genome Res 2003, 13:1904-1915.
27. Lucy Demonstration Data Set [http://www.tigr.org/software/ sequencing.shtml]
28. MySQL [http://www.mysql.com]
29. PostgreSQL [http://www.postgresql.org]