TopHat is an efficient read-mapping algorithm designed to align reads from an RNA-Seq experiment to a reference genome without relying on known splice sites. However, current software for aligning RNA-Seq data to a genome relies on known splice junctions and cannot identify novel ones. These fragments, or 'reads', can be used to measure levels of gene expression and to identify novel splice variants of genes.
A new protocol for sequencing the messenger RNA in a cell, known as RNA-Seq, generates millions of short sequence fragments in a single run.
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