ProbeLynx

ProbeLynx evaluates microarray probe sequences against current genomic sequence data to assess probe specificity and update gene and transcript functional annotations for accurate microarray-based transcript measurement.

Key Features:

• Probe Specificity Assessment: Accepts probe sequences in FASTA format (oligonucleotide or cDNA) and compares them to up-to-date genomic sequences to assess specificity and identify potential cross-hybridization with paralogous genes.
• Functional Annotation Updates: Integrates gene function annotations from Ensembl and TIGR to update transcript- and gene-level annotations associated with each probe.
• Tab-delimited Output: Produces results as a tab-delimited flat file for integration into spreadsheet applications or database management systems.
• Genomic Dataset Flexibility: Supports analyses for human, mouse, chicken, and bovine genomes and can be adapted to additional genomic datasets.

Scientific Applications:

• Microarray probe re-annotation: Re-annotating microarray probe sets to reflect current genomic sequences and gene predictions.
• Gene expression reliability: Reducing false signals in gene expression studies by identifying cross-hybridizing probes and updating probe-target mappings.
• Transcriptomics and functional genomics: Facilitating analyses in genomics, transcriptomics, and functional genomics across human, mouse, chicken, and bovine datasets.

Methodology:

Compares input FASTA probe sequences (oligonucleotide or cDNA) to genomic sequence data to assess specificity and detect paralogous cross-hybridization, integrates Ensembl and TIGR gene function annotations, and outputs results as a tab-delimited flat file.