AntiHunter 2.0

AntiHunter 2.0 identifies expressed sequence tag (EST) antisense transcripts within specified genomic regions by analyzing BLAST output to detect natural antisense transcripts (NATs) involved in gene regulation and disease.

Key Features:

• Enhanced Detection Capability: Detects over 45% more antisense ESTs compared with the predecessor without a corresponding increase in false positives.
• Increased Query Size: Supports maximum query sizes increased from 1 Mb to 3 Mb and, when using MEGABLAST, accepts sequences up to 30 Mb.
• BLAST Query Options: Offers BLASTN and MEGABLAST for EST database querying, with MEGABLAST providing a trade-off between sensitivity and allowable query size.
• Repeat Masking and EST Analysis: Masks repetitive regions in the genomic sequence and analyzes BLAST output against EST databases to identify ESTs aligning antisense to known transcripts.

Scientific Applications:

• Gene Regulation Studies: Identification of NATs supports investigation of their roles in gene expression regulation.
• Disease Research: Detection of antisense transcription can inform studies of mechanisms and potential therapeutic targets in human diseases.
• Genomic Annotation: Aids genome annotation by revealing previously unrecognized antisense transcripts.

Methodology:

The workflow masks repetitive regions in the input genomic sequence, performs BLASTN or MEGABLAST searches against an EST database, and analyzes BLAST output to identify ESTs that align antisense to known transcripts.