CleanBSequences

CleanBSequences removes adaptor and cloning-vector-derived sequences from PCR-amplified biological sequence datasets to automate curation for AFLP, cDNA-AFLP, and MSAP-based genomic, transcriptomic, and epigenomic studies.

Key Features:

• Alignment-based trimming: Aligns forward and/or reverse primers or cloning vector ends to target sequences to identify and remove adaptor and undesired fragments.
• Adaptor removal for PCR amplification: Detects and excises adaptor sequences used for PCR amplification from sequence reads.
• Subsequence retention: Retains necessary target subsequences after trimming to preserve biological signal.
• High-throughput processing: Processes large datasets rapidly and accurately for omic-scale studies.
• R package implementation: Implemented as an R package for integration into R-based bioinformatics workflows.
• Error reduction: Automates curation to reduce errors associated with manual sequence trimming.

Scientific Applications:

• Molecular marker preprocessing: Cleans sequence data from AFLP, cDNA-AFLP, and MSAP experiments prior to downstream analysis.
• Omic data curation: Prepares genomic, transcriptomic, and epigenomic datasets by removing adaptor and cloning-vector contamination.
• Sequence analysis preparation: Streamlines downstream sequence analysis workflows by standardizing trimmed sequences.

Methodology:

Aligns forward and/or reverse primers or cloning vector ends to target sequences and removes matching adaptor and undesired fragments while retaining target subsequences.