Bio::SAGE::DataProcessing 1.20

Bio::SAGE::DataProcessing module processes raw serial analysis of gene expression (SAGE) data.

SYNOPSIS

use Bio::SAGE::DataProcessing;
$sage = Bio::SAGE::DataProcessing->new();

# open sequence and quality files
open( READS, "library.fasta" );
open( QUAL, "library.qual.fasta" );

# collect ditags and statistics from reads
$sage->process_library( *READS, *QUAL );

# close files
close( READS );
close( QUAL );

# output tags in descending order of expression
my %tags = %{$sage->get_tagcounts()};
open( TAGS, ">library.tags" );
map { print TAGS join( "t", $_, $tags{$_} ) . "n" } sort { $tags{$b} <=> $tags{$a} } keys %tags;
close( TAGS );

# tag AAACCGGGTT matches two different genes
# so 15th base pair may help resolve this
$sage->print_extra_base_calculation( $sage->get_extract_base_calculation( "AAACCGGGTT" ) );

This module provides several tools for processing and analyzing serial analysis of gene expression (SAGE) libraries.

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.