Bio::SAGE::Comparison Bio::SAGE::Comparison module compares data from serial analysis of gene expression (SAGE) libraries.
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Perl module gene analysis SAGE analysis gene SAGE

Bio::SAGE::Comparison Description

Bio::SAGE::Comparison module compares data from serial analysis of gene expression (SAGE) libraries. Bio::SAGE::Comparison module compares data from serial analysis of gene expression (SAGE) libraries.SYNOPSIS use Bio::SAGE::Comparison; $sage = Bio::SAGE::Comparison->new();This module provides several tools for comparing data generated from serial analysis of gene expression (SAGE) libraries.BACKGROUNDSerial analysis of gene expression (SAGE) is a molecular technique for generating a near-global snapshot of a cell population’s transcriptome. Briefly, the technique extracts short sequences at defined positions of transcribed mRNA. These short sequences are then paired to form ditags. The ditags are concatamerized to form long sequences that are then cloned. The cloned DNA is then sequenced. Bioinformatic techniques are then employed to determine the original short tag sequences, and to derive their progenitor mRNA. The number of times a particular tag is observed can be used to quantitate the amount of a particular transcript. The original technique was described by Velculescu et al. (1995) and utilized an ~14bp sequence tag. A modified protocol was introduced by Saha et al. (2002) that produced ~21bp tags.PURPOSEThis module facilitates the comparison of SAGE libraries. Specifically: 1. Calculations for determining the statistical significance of expression differences. 2. Dynamically convert longer-tag libraries to a shorter type for comparison (e.g. comparing a LongSAGE vs. a regular SAGE library).Both regular SAGE (14mer tag) and LongSAGE (21mer tag) are supported by this module.Statistical significance in library comparisons is calculated using the method described by Audic and Claverie (1997). Code was generated by directly porting the authors' original C source.Requirements:· Perl

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