VarDetect: A nucleotide sequence variation exploratory tool

BMC Bioinformatics

Volumn 9, Issue SUPPL. 12, 2008, Pages

  Ngamphiw, Chumpol ^a   Kulawonganunchai, Supasak ^b   Assawamakin, Anunchai ^c   Jenwitheesuk, Ekachai ^a   Tongsima, Sissades ^a  

^a NATIONAL SCIENCE AND TECHNOLOGY DEVELOPMENT AGENCY   (Thailand)

^b ASIAN INSTITUTE OF TECHNOLOGY   (Thailand)

^c MAHIDOL UNIVERSITY   (Thailand)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEX DISEASE; DETECTION EFFICIENCY; DETECTION TOOLS; GENE MUTATIONS; GENETIC VARIATION; NUCLEOTIDE SEQUENCES; NUCLEOTIDE VARIATION; SINGLE NUCLEOTIDE POLYMORPHISMS; CONTENT RATIO; DNA SAMPLES; HUMAN GENES; MICROSOFT WINDOWS;

CHROMATOGRAPHIC ANALYSIS; COMPUTER SOFTWARE; FLUORESCENCE; GENE ENCODING; TOOLS; COMPUTER OPERATING SYSTEMS; NUCLEOTIDES;

NUCLEOTIDES; BIOINFORMATICS;

ARTIFACT; AUTOMATION; CHROMATOGRAPHY; COMPUTER PROGRAM; CONFERENCE PAPER; CONTROLLED STUDY; DNA DETERMINATION; DNA SEQUENCE; FLUORESCENCE ANALYSIS; GENE IDENTIFICATION; INTERMETHOD COMPARISON; INTERNET; NUCLEOTIDE SEQUENCE; PROTEIN VARIANT; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; ARTICLE; BIOLOGY; CHEMISTRY; GENETIC PREDISPOSITION; GENETIC VARIABILITY; GENOMICS; HUMAN; LABORATORY DIAGNOSIS; METHODOLOGY; REPRODUCIBILITY; STATISTICAL ANALYSIS;

NUCLEOTIDE;

AUTOMATION; BASE SEQUENCE; CHROMATOGRAPHY; COMPUTATIONAL BIOLOGY; DATA INTERPRETATION, STATISTICAL; FALSE POSITIVE REACTIONS; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; GENOMICS; HUMANS; NUCLEOTIDES; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 57649166523     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-S12-S9     Document Type: Conference Paper

References (19)

1. Uda M Galanello R Sanna S Lettre G Sankaran V Chen W Usala G Busonero F Maschio A Albai G Genome-wide association study shows BCL11A associated with persistent fetal hemoglobin and amelioration of the phenotype of beta-thalassemia Proc Natl Acad Sci USA 2008, 105:1620-1625 2234194 18245381 10.1073/pnas.0711566105
2. Kozyrev S Abelson A Wojcik J Zaghlool A Linga Reddy M Sanchez E Gunnarsson I Svenungsson E Sturfelt G Jonsen A Functional variants in the B-cell gene BANK1 are associated with systemic lupus erythematosus Nat Genet 2008, 40:211-216 10.1038/ng.79 18204447
3. Pandya G Holmes M Sunkara S Sparks A Bai Y Verratti K Saeed K Venepally P Jarrahi B Fleischmann R A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip whole-genome resequencing platform Nucleic Acids Res 2007, 35:e148 2175352 18006572 10.1093/nar/gkm918
4. Adzhubei A Laerdahl J Vlasova A preAssemble: A tool for automatic sequencer trace data processing BMC Bioinformatics 2006, 7:22 1352386 16417643 10.1186/1471-2105-7-22
5. Prosdocimi F Lopes D Peixoto F Mourao M Pacifico L Ribeiro R Ortega J Effects of sample re-sequencing and trimming on the quality and size of assembled consensus sequences Genet Mol Res 2007, 6:756-765 18058703
6. Ewing B Green P Base-calling of automated sequencer traces using phred. II. Error probabilities Genome Res 1998, 8:186-194 9521922
7. Common sequencing artifacts http://seqcore.brcf.med.umich.edu/doc/dnaseq/ trouble/badseq.html
8. Mutation Surveyor http://www.softgenetics.com/ms/
9. Ewing B Hillier L Wendl M Green P Base-calling of automated sequencer traces using phred. I. Accuracy assessment Genome Res 1998, 8:175-185 9521921
10. Nickerson D Tobe V Taylor S PolyPhred: Automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing Nucleic Acids Res 1997, 25:2745-2751 146817 9207020 10.1093/ nar/25.14.2745
11. Weckx S Del-Favero J Rademakers R Claes L Cruts M De Jonghe P Van Broeckhoven C De Rijk P novoSNP, a novel computational tool for sequence variation discovery Genome Res 2005, 15:436-442 551570 15741513 10.1101/ gr.2754005
12. Takahashi M Matsuda F Margetic N Lathrop M Automated Identification of Single Nucleotide Polymorphisms from Sequencing Data J Bioinform Comput Biol 2003, 1:253-265 10.1142/S021972000300006X 15290772
13. F-score calculation http://en.wikipedia.org/wiki/F-score
14. Tocharoentanaphol C Promso S Zelenika D Lowhnoo T Tongsima S Sura T Chantratita W Matsuda F Mooney S Sakuntabhai A Evaluation of resequencing on number of tag SNPs of 13 atherosclerosis-related genes in Thai population J Hum Genet 2007, 53:74-86 10.1007/s10038-007-0220-8 18043865
15. ThaiSNP database http://www.biotec.or.th/thaisnp
16. 4peaks software http://mekentosj.com/4peaks/
17. FinchTV software http://www.geospiza.com/finchtv/
18. Stajich J Block D Boulez K Brenner S Chervitz S Dagdigian C Fuellen G Gilbert J Korf I Lapp H The Bioperl toolkit: Perl modules for the life sciences Genome Res 2002, 12:1611-1618 187536 12368254 10.1101/gr.361602
19. Mangalam H The Bio* toolkits - a brief overview Brief Bioinform 2002, 3:296-302 10.1093/bib/3.3.296 12230038