WebTraceMiner

WebTraceMiner processes raw Expressed Sequence Tag (EST) trace files to detect sequence features and enable cDNA termini characterization, EST data validation, and sequence data mining.

Key Features:

• Sequence Feature Detection: Detects vector fragments, adapter/linker sequences, insert‑flanking restriction endonuclease recognition sites, and polyA or polyT tails within EST trace files.
• Data Validation: Identifies and facilitates removal of vector and adapter/linker sequences and polyA/polyT tails to preserve accurate positional information for posttranscriptional modifications such as polyadenylation.
• Data Mining of Public Traces: Reanalyzes raw DNA sequence data from the NCBI Trace Archive to uncover novel functional motifs and information in error‑prone ESTs.

Scientific Applications:

• cDNA termini characterization: Enables accurate mapping of 3' and 5' cDNA insert boundaries in EST datasets by detecting terminal features.
• Gene expression and novel gene discovery: Supports studies of gene expression patterns and identification of novel genes from EST traces.
• Functional motif discovery: Facilitates detection of functional motifs and posttranscriptional modification signals such as polyadenylation sites within ESTs.

Methodology:

Processes raw EST trace files; detects vector fragments, adapter/linker sequences, insert‑flanking restriction endonuclease recognition sites, and polyA/polyT tails; removes vector/adapter sequences and polyA/polyT tails; and reanalyzes raw DNA sequence data from the NCBI Trace Archive.