Bio::SAGE::DataProcessing README

#
# 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 $
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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.

