PLANdbAffy

PLANdbAffy maps and annotates 25-mer oligonucleotide Affymetrix microarray probe sequences from five Affymetrix expression arrays to the human genome and catalogs corresponding mRNA and expressed sequence tag (EST) sequences and single nucleotide polymorphisms (SNPs) to improve interpretation of gene expression measurements.

Key Features:

• Genome alignments: Aligns probe sequences from five Affymetrix expression microarrays against the human genome.
• Probe orientation and transcript mapping: Identifies probes that align to transcript-coding regions in the correct orientation.
• mRNA and EST cataloging: Determines and catalogs mRNA and EST sequences that contain each probe sequence.
• SNP annotation: Summarizes SNPs located within probe alignment regions.
• Probe quality flags: Flags probes potentially affected by cross-hybridization, intronic mapping, or alternative splicing.
• UCSC Genome Browser integration: Provides custom tracks for visualization within the UCSC Genome Browser.

Scientific Applications:

• Microarray expression accuracy: Improves accuracy and reliability of gene expression analyses derived from Affymetrix microarrays by providing probe-level genomic context.
• Variant and transcript impact assessment: Identifies probes whose signals may be influenced by SNPs, alternative splicing, intronic mapping, or cross-hybridization.
• Genomics and transcriptomics interpretation: Supports interpretation of probe alignments in genomic and transcriptomic studies via UCSC Genome Browser context.

Methodology:

Detailed alignment of probe sequences against the human genome; identification of probes aligning to transcript-coding regions in correct orientation; determination and cataloging of mRNA and EST sequences containing probe sequences; summarization of sequences covering probe alignment regions and any SNPs located within these regions; integration of custom tracks into the UCSC Genome Browser.