MMSEQ

MMSEQ estimates isoform expression and allelic imbalance in diploid organisms from RNA-seq data.

Key Features:

• Haplotype-Specific Isoform Modeling: Models expression of haplotype-specific isoforms to quantify allele-specific transcript abundance in diploid organisms.
• Reconstruction of Parental Isoform Sequences: Reconstructs parental isoform sequences directly from RNA-seq data when parental sequences are unavailable.
• Deconvolution of Read Mapping: Deconvolves mapping of sequencing reads to multiple transcripts, including standard isoforms and haplotype-specific variants, to attribute reads to transcripts.
• Handling Non-Uniform Read Generation: Accounts for non-uniform read generation in RNA-seq to reduce bias in expression estimates.
• Compatibility with Paired-End Reads: Supports analysis of paired-end RNA-seq reads.

Scientific Applications:

• Functional Genomics: Provides isoform-level expression estimates to study transcript function within biological pathways.
• Genetic Studies: Detects allelic imbalance to investigate genetic contributions to phenotypic variation and disease susceptibility.
• Evolutionary Biology: Analyzes haplotype-specific expression patterns to study evolutionary processes and genetic diversity.

Methodology:

Implements a novel statistical methodology to simultaneously estimate isoform expression and allelic imbalance, deconvolves read mapping to multiple transcripts including haplotype-specific variants, reconstructs parental isoform sequences from RNA-seq when needed, accounts for non-uniform read generation, and supports paired-end reads.