:: DESCRIPTION
PDA ( Pooled DNA analyzer ) is a powerful tool for analyses of pooled DNA data.
::DEVELOPER
Hsin-Chou Yang and Cathy SJ Fann(Institute of Biomedical Sciences, Academia Sinica, Taiwan)
:: SCREENSHOTS
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hsin-Chou Yang, Chia-Ching Pan, Chin-Yu Lin and Cathy SJ Fann (2006).
PDA: pooled DNA analyzer.
BMC Bioinformatics, 7: 233.
:: DESCRIPTION
SPLINTER (Short IN/DEL Prediction by Large deviation Inference and Non-linear True frequency Estimation by Recursion) is a software which detects and quantifies short IN/DELs as well as single nucleotide substitutions in pooled-DNA samples. SPLINTER can accurately detect rare variants in large pools, providing a novel and sensitive method that will allow for significant progress in the discovery of novel disease-causing rare variants from DNA pools of affected individuals, such as germ-line mutation discovery for breast and ovarian cancer patients.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Genome Res. 2010 Dec;20(12):1711-8. doi: 10.1101/gr.109157.110.
High-throughput discovery of rare insertions and deletions in large cohorts.
Vallania FL, Druley TE, Ramos E, Wang J, Borecki I, Province M, Mitra RD.
:: DESCRIPTION
vipR is a program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms.
::DEVELOPER
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
vipR: variant identification in pooled DNA using R.
Altmann A, Weber P, Quast C, Rex-Haffner M, Binder EB, Müller-Myhsok B.
Bioinformatics. 2011 Jul 1;27(13):i77-84. doi: 10.1093/bioinformatics/btr205.
:: DESCRIPTION
PDA, Pipeline Diversity Analysis, is a collection of programs and modules, mainly written in Perl, that automatically can:
explore for potentially polymorphic sequences from a large source of heterogeneous DNA,
extract and sort them out by gene, species and extent of similarity,
align the different groups, and
estimate the genetic diversity in different functional regions.
::DEVELOPER
Sònia Casillas and Antonio Barbadilla. Genomics, Bioinformatics and Evolution Group.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Sònia Casillas and Antonio Barbadilla (2006).
PDA v.2: improving the exploration and estimation of nucleotide polymorphism in large datasets of heterogeneous DNA.
Nucleic Acids Res. 34 (Web Server issue): W632-W634; doi: 10.1093/nar/gkl080
:: DESCRIPTION
MPDA (Microarray Pooled DNA Analyzer) is an innovative tool for analyzing hybridization intensity data from microarray-based pooled DNA experiments. Graphic and numerical outputs from MPDA support global and detailed inspection for bulk of genomic data.
::DEVELOPER
Hsin-Chou Yang and Cathy SJ Fann(Institute of Biomedical Sciences, Academia Sinica, Taiwan)
:: SCREENSHOTS
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hsin-Chou Yang, Mei-Chu Huang, Ling-Hui Li, Chien-Hsing Lin, Alice L. T. Yu, Mitchell B. Diccianni, Jer-Yuan Wu, Yuarn-Tsong Chen, Cathy S. J. Fann (2008).
MPDA: Microarray Pooled DNA Analyzer.
BMC Bioinformatics. 9:196.
