PALMapper

PALMapper computes unspliced and spliced alignments of RNA-Seq reads to support transcriptome reconstruction and gene structure identification.

Key Features:

• Dual Alignment Capability: Computes both unspliced and spliced alignments for RNA-Seq reads to capture exon–intron structure.
• Integration of GenomeMapper and QPALMA: Combines GenomeMapper’s mapping capabilities with QPALMA’s algorithms that use read-quality information and splice site predictions.
• High-Throughput Performance: Processes millions of RNA-Seq reads to support large-scale sequencing datasets.

Scientific Applications:

• Transcriptome Reconstruction: Accurately aligns short and error-prone RNA-Seq reads across intron boundaries to facilitate detailed transcript reconstruction.
• Gene Structure Identification: Produces spliced alignments that enable identification of exon–intron organization and gene structures.

Methodology:

Combines GenomeMapper for efficient mapping with QPALMA algorithms that incorporate read-quality information and splice site predictions to compute unspliced and spliced alignments.