Bio::SAGE::DataProcessing README

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# Copyright (c) 2004 Scott Zuyderduyn <scottz@bccrc.ca>. # All rights reserved. This program is free software; you # can redistribute it and/or modify it under the same # terms as Perl itself.
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# $Id: README,v 1.1.1.1 2004/05/24 02:52:55 scottz Exp $ #

BACKGROUND

Serial 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.

PURPOSE

This module facilitates the processing of SAGE data. Specifically:

  1. extracting ditags from raw sequence reads.
  2. extracting tags from ditags, with the option to exclude tags if the Phred scores (described by Ewing and Green, 1998a and Ewing et al., 1998b) do not meet a minimum cutoff value.
  3. calculating descriptive values
  4. statistical analysis to determine, where possible, additional nucleotides to extend the length of the SAGE tag (thus facilitating more accurate tag to gene mapping).

Both regular SAGE (14mer tag) and LongSAGE (21mer tag) are supported by this module. Future protocols should be configurable with this module.

REFERENCES

Velculescu V, Zhang L, Vogelstein B, Kinzler KW. (1995) Serial analysis of gene expression. Science. 270:484-487.

Saha S, Sparks AB, Rago C, Akmaev V, Wang CJ, Vogelstein B, Kinzler KW, Velculescu V. (2002) Using the transcriptome to annotate the genome. Nat. Biotechnol. 20:508-512.

Ewing B, Hillier L, Wendl MC, Green P. (1998a) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8:175-185.

Ewing B, Green P. (1998b) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8:186-194.