PromoSer

PromoSer extracts and analyzes proximal promoter sequences from human, mouse, and rat genomes to support studies of transcriptional regulation.

Key Features:

• Species coverage: Supports proximal promoter extraction for human, mouse, and rat genes.
• TSS identification: Identifies transcription start sites by mapping mRNA and expressed sequence tag (EST) sequences against genomic DNA.
• Partial and full-length mRNA handling: Alignments account for both partial and full-length mRNA sequences to detect TSS and alternative promoters.
• Sequence filtering and alignment clustering: Applies initial filtering to raw mRNA/EST sequences and uses alignment clustering algorithms to improve TSS prediction reliability.
• Batch retrieval: Enables retrieval of large sets of proximal promoters for high-throughput analyses.
• Database performance: Employs an optimized underlying database for efficient access and retrieval of promoter data for large datasets.
• Programmatic access: Supports SOAP-based queries and returns XML-formatted responses for integration into bioinformatics pipelines.

Scientific Applications:

• Genomic promoter annotation: Retrieval of proximal promoters for genome-wide promoter annotation and cataloging.
• Transcriptional regulation studies: Identification of TSS and alternative promoters to investigate promoter usage and regulatory mechanisms.
• Comparative and co-regulation analyses: Batch promoter retrieval for analyses of co-regulated gene sets and comparative promoter sequence studies.

Methodology:

Maps mRNA and EST sequences to genomic DNA, applies initial sequence filtering, clusters alignments, accounts for partial and full-length mRNA to identify TSS including alternative promoters, and provides results via a SOAP interface with XML responses.