Seq2Fun

Seq2Fun performs ultra-fast functional profiling of RNA-seq reads to quantify gene and pathway abundance for experiments including non-model organisms without reference genomes.

Key Features:

• Ultra-Fast Processing: Processes over 2 million reads per minute and is reported to be more than 120 times faster than workflows relying on de novo transcriptome assembly.
• Direct Functional Quantification: Performs functional quantification directly on reads while bypassing de novo transcriptome assembly and reducing file I/O.
• Comprehensive Pipeline: Implements raw read quality control including sequencing error correction, poly(A) tail removal, and joining overlapped paired-end reads; translates reads into all possible amino acid fragments and performs DNA-to-protein searches against a curated protein database; and produces gene abundance tables, pathway and species hit tables, an HTML report, and annotated clean reads.
• Efficiency on Standard Hardware: Implemented in C++ and optimized to run on personal computers with limited CPU and memory resources.

Scientific Applications:

• Functional profiling of non-model organisms: Enables rapid gene expression analysis, pathway elucidation, and species identification from RNA-seq data when reference genomes are unavailable and generates outputs for downstream analyses.

Methodology:

Performs raw read quality control (sequencing error correction, poly(A) removal, joining overlapped paired-end reads), translates each read into all possible amino acid fragments, conducts DNA-to-protein homology searches against a curated protein database, and directly quantifies functional features from read-level matches; implemented in C++ and optimized for limited CPU and memory.