Mesalina

Mesalina maps cDNA sequences and identifies splice sites to provide fast, sensitive spliced alignment of short and long reads.

Key Features:

• High Accuracy: Provides precise alignment of cDNA sequences, including detection of novel non-canonical splice sites.
• Robust Performance: Maintains sensitivity and accuracy as read length increases for both short and long reads.
• Speed and Efficiency: Uses a seed-extend strategy combining rapid retrieval of maximal exact matches with a sandwich dynamic programming algorithm, yielding more than ten times faster performance than other mappers with comparable accuracy.

Scientific Applications:

• cDNA mapping and splice identification: Mapping cDNA and identifying splice junctions in sequencing reads.
• Novel splice site discovery: Detection of novel non-canonical splice sites from aligned reads.
• Read-length scalable spliced alignment: Sensitive spliced alignment applicable to both short and long reads.

Methodology:

Implements a seed-extend strategy that rapidly retrieves maximal exact matches and applies a sandwich dynamic programming algorithm for sensitive alignment of spliced reads.