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POSA: Perl Objects * for DNA Sequencing Data Analysis

POSA: Perl Objects * for DNA Sequencing Data Analysis. 生科系 林祐任. Background. Capillary Electrophoresis. Background. Pipeline : Instruction scheduling on Intel Pentium 4. Implementation. Results:Functionality. to design and implement automated sequencing data analysis .

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POSA: Perl Objects * for DNA Sequencing Data Analysis

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  1. POSA: Perl Objects* for DNA Sequencing Data Analysis 生科系 林祐任

  2. Background • Capillary Electrophoresis

  3. Background • Pipeline: Instruction scheduling on Intel Pentium 4.

  4. Implementation

  5. Results:Functionality • to design and implement automated sequencing data analysis. • Finally, data can be stored in objects, or in files in either exp, scfor fastaformat.

  6. Results:Functionality • Examples of possible analysis pipelines: include BAC-end sequencing +automated PCR primer design for chromosome walking /resequencingof PCR products with SNP annotation /for SNP genotyping /for SNP discovery /SBE primer design

  7. Results:Performance • from several hours to a few minutes • highly consistent with manual editing. • sequence analysis tools like Phred, Phrapand PolyPhred.

  8. Results:Intended use and benefits for users • easy &highly automated DNA sequence and contig data analysis /popular tools. • reduces analysis time • allowing code improvements by the user community.

  9. Conclusions • POSA describes a DNA sequence read and a Phrapcontig assembly in detail. • flexible and easy setup of perl-based pipelines to handle DNA sequencing data, including generating primer3 input and automated SNP discovery, while requiring only little programming skills

  10. Capillary electrophoresis (CE), also known as capillary zone electrophoresis (CZE), can be used to separate ionic species by their charge and frictional forces and hydrodynamic radius.

  11. In computer science, instruction scheduling is a compiler optimization used to improve instruction-level parallelism, which improves performance on machines with instruction pipelines. • Compiler optimization is the process of tuning the output of a compiler to minimize or maximize some attributes of an executable computer program. The most common requirement is to minimize the time taken to execute a program

  12. The Read.pm object describes a DNA sequence trace and includes methods for data import from a variety of formats • The Contig.pm object contains a method to assemble contigs of reads using the Phrapprogram [6]. • 基因組定序的策略可以分成幾個方式： -由下而上圖譜繪製(bottom-up  mapping) -由上而下圖譜繪製(top-down  mapping) -染色體步行術(chromosome  walking)

  13. The phred software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base. • phrapis a program for assembling shotgun DNA sequence data(In genetics, shotgun sequencing, also known as shotgun cloning, is a method used for sequencing long DNA strands. It is named by analogy with the rapidly-expanding, quasi-random firing pattern of a shotgun.) • PolyPhred is a program that compares fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions.

  14. Primer3 is a widely used program for designing PCR primers

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