SAGE Suite

Institutions

Downloads

In this section you can find all the newest versions of SAGE Analysis and the SAGE GenSuite. Some additional scripts for analysis and debugging are also available.

SAGE GenSuite

Here you can find all the modules of the SAGE GenSuite for download.

genSuite.pl [Version 0.49]
The graphical vertion of the genSuite package. Contains all modules separetad in tabs to easy use. Accepts importation of data em may save any part of the process. The package Perl/Tk (found in http://www.bribes.org/perl/ppmdir.html) is required. For the use of the GIG distribution the package R (http://www.r-project.org/) is required, as is the GIG generator module, found here.

GenSuite Package [Version 0.41]
This is the whole suite in a tar format.

tag_count_generator.pl [Version 0.53]
This program generates a list of random tags with a user-defined size and random counts. Counts may be uniform, or follow a Gaussian (Normal) or Gamma distributions.

trim_tags.pl [Version 0.45]
Given a tag count file, this program generates a new list of tags and counts count where a user-defined percentage of the tags have had their 3' end base trimmed off. This is useful to simulate some restriction enzymes that do not cut uniformily. It can also be used to define all tags to a given size.

counts2ditags.pl [Version 0.52]
Given a list of tags and countsm this program creates a new file containing a list of ditags. Tag joining can be done assuming either a blunt-end or overlapping bases, as defined by the user.

repeated_ditag_evaluator.pl [Version 0.35]
An opitional step in the pipeline, used to calculate the real expected ditags frequency in the ditags pool. Using stocastics aproaches we can determinate if the amount of ditags in the data is within a aceptable threshold and gerenates a full report for analysis. From this it's generated a new set of ditags, without the ditags within the threshold, or eliminates all the repetition, according to the parameters.

ditags2concatamers.pl [Version 0.5]
This program uses a list of ditags to generate a multiple sequence FASTA file containing concatamers. Random-size flanking ends can also be generated.

GenSuite Presentation [For Version 0.3]
A short presentation showing the basics of the suite with some examples.

SAGE Analysis

analysis.pl [Version 0.48]
The graphical vertion of the SAGE Analysis package. Contains all modules separetad in tabs to easy use. Accepts importation of data em may save any part of the process. The package Perl/Tk (found in http://www.bribes.org/perl/ppmdir.html) is required. For the use of the background run the package "threads" is also required.

SAGE Analysis Package [Version 0.41]
The complete SAGE analysis package comprising the programs below.

extract_ditags.pl [Version 0.46]
This component extracts ditags from a multiple sequence (concatamers) FASTA file and is able to deal with punctuation site (CATG) errors.

extract_tags.pl [Version 0.46]
 This componente extracts the tags from a list of ditag sequences and provides the respective counts.

sage_analysis.pl [Version 0.43]
This script integrates extract_ditags.pl and extract_tags.pl components and generates a set of reports.

kempbasushell.pl [Version 0.41]
For the Analysis of the data extracted from the tags a statistical program must be used. For that proupose this shell help to set up the data for the Kemp/Basu analysis, that calculates the correlation betwen two or more lybraries by frequentist or Bayesian tests.

statsConcat.pl [Version 0.2]
An extra script used to make tests on the size of the ditags from the concatamers. Used to validate the size extracted by concatemers.pl.

Extra files

compareCounts.pl [Version 0.32]
A simple script that compares two counts in the SAGE Suite standard format and generates reports files with the diferences and semelhances between then.

separeDitags.pl [Version 0.1]
For data like Long-SAGE where many size ditags are formed is needed to separe the diferent seized ditags. That is the function of this script, it generates diferent files with the ditags of same sizes.