CPTRA

CPTRA performs integrated transcriptome analysis by combining long-read 454 pyrosequencing and short-read Illumina Genome Analyzer (Solexa) sequence tag datasets to enable gene expression profiling and functional annotation in species lacking reference genomes.

Key Features:

• Cross-Platform Integration: Integrates data from multiple NGS platforms, including 454 pyrosequencing and Illumina Genome Analyzer (Solexa), to broaden transcriptome coverage in species with limited genomic information.
• Data Processing Capabilities: Processes annotated long-read sequences and short-read sequence tags as dual inputs for integrated analysis.
• Unique Sequence Tag Identification: Identifies unique sequence tags to distinguish individual transcripts within complex mixtures.
• Tag Counting and Quantification: Performs tag counting to quantify transcript abundance and support expression profiling.
• Cross-Platform Sequence Matching: Matches short sequence tags to annotated long reads and annotates tags with functional information, expression levels, and Gene Ontology (GO) classifications.
• Multiple Sequence Search Algorithms: Implements various sequence search algorithms to enable comparison of matching methods.

Scientific Applications:

• Transcriptome profiling without reference genomes: Enables global gene expression profiling and functional annotation in species lacking comprehensive genome sequences.
• Non-target site glyphosate resistance in horseweed: Applied to identify transport genes associated with glyphosate resistance and to nominate candidate genes for further study.

Methodology:

Combines long-read and short-read sequencing data from multiple NGS platforms (454 pyrosequencing, Illumina Genome Analyzer/Solexa); identifies unique sequence tags, performs tag counting for quantification, annotates tags with functional information including Gene Ontology classifications, and matches short sequence tags to annotated long reads using multiple sequence search algorithms.