Download Shareware and Freeware Software for Windows, Linux, Macintosh, PDA

line Home  |  About Us  |  Link To Us  |  FAQ  |  Contact

Serving Software Downloads in 976 Categories, Downloaded 29.872.504 Times

Bio::SAGE::DataProcessing 1.20

  Date Added: June 16, 2010  |  Visits: 720


Report Broken Link
Printer Friendly Version

Product Homepage
Download (76 downloads)

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..

Requirements: No special requirements
Platforms: Linux
Keyword: Analysis Biosagedataprocessing Dataprocessing Expression Gene Gene Expression Libraries Module Qual Reads Sage Serial Analysis Of Gene Expression Tag Tags
Users rating: 0/10

License: Freeware Size: 19.46 KB
More Reviews or Write Review

Libraries  -  Bio::SAGE::Comparison 1.00
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...
8.19 KB  
Multimedia & Graphics  -  BCLUST New
BCLUST is a small, simple, command prompt based tool specially designed to help you asses reliability of gene clusters from expression data by using consensus tree and bootstrap resampling method. Because of the rapid development of microarray...
Education  -  ErmineJ 2.1.21
ErmineJ performs analyses of gene sets in expression microarray data or other genome-wide data that results in rankings of genes. A typical goal is to determine whether particular biological pathways are "doing something interesting" in the data....
21.13 MB  
Multimedia & Graphics  -  CLC Main Workbench 6.5 Build 65005
Main Workbench includes all features from CLC DNA Workbench, CLC RNA Workbench, and CLC Protein Workbench, as well as a range of Gene Expression Analysis. CLC Main Workbench creates a software environment enabling users to make a large number of...
Development Tools  -  DNA MicroArray Image Processing Case Study 1.0
In one type of gene expression analysis, fluorescently tagged messenger RNA from different cells are hybridized to a microscopic array of thousands of complimentary DNA spots that correspond to different genes. Illuminated spots emit different...
4.35 MB  
Education  -  EMOGEE 1.0
Recent studies describe that the level of gene expression between species is positively correlated with the time that has passed since the species split from a common ancestor (Ranz et al., 2006). Moreover, Khaitovich et al. (2004) found a linear...
829.44 KB  
Libraries  -  Language::Basic::Expression 1.44
Language::Basic::Expression is a Perl package to handle string, numeric, and boolean expressions. SYNOPSIS See Language::Basic for the overview of how the Language::Basic module works. This pod page is more technical. # Given an...
52.22 KB  
Science  -  Maple Tree
Maple Tree is a Java based visualization tool used by researchers in the biological sciences to visualize and graphically browse the results of analyses of gene expression data collected from microarray experiments.
1.17 MB  
Science  -  Nuclear Simulation Java Class Libraries rc
The class libraries here provide infrastructure for creating simulations of low energy nuclear physics experiments, as well as some useful working programs that do simple simulations and analysis of experiments performed with magnetic spectrographs.
1.3 MB  
Libraries  -  XML::DocStats 0.01
XML::DocStats is a Perl module to produce a simple analysis of an XML document. SYNOPSIS Analyze the xml document on STDIN, the STDOUT output format is html: use XML::DocStats; my $parse = XML::DocStats->new; $parse->analyze; Analyze...
27.65 KB  
Programming  -  FLEX-db Digital Asset Manager 3.0.9
FLEX-db - an enterprise Digital Asset Manager (DAM). It ingests and links metadata with files, creates thumbnails, and processes files using business rules. FLEX-db has a JSP client, Java app server for file input and output and an EJB metadata...
21.57 MB  
Programming  -  Libicom 0.9.0
The libicom library is a character based dynamicly linked library for Linux. It is used to remotely control the Icom IC-R8500 wide band receiver via an RS232 link. All call and return parameters to the control functions are character string based....
20.48 KB  
Programming  -  dotdesktop 0.3
Dotdesktop library provides ability to parse desktop entry file and access the information in a convenient way. Desktop entry file format is defined by, it is used to describe information about an application such as the name and...
327.68 KB  
Programming  -  Cedalion for Linux 0.2.6
Cedalion is a programming language that allows its users to add new abstractions and define (and use) internal DSLs. Its innovation is in the fact that it uses projectional editing to allow the new abstractions to have no syntactic limitations.
471.04 KB  
Programming  -  libyasl 0.2
Libyasl is a C++ class library to easily realize TCP/UDP/Multicast clientsand servers in IPv4 and IPv6 environments under GNU/Linux systems.
143.36 KB  
Libraries  -  wolfSSL 3.11.0
The wolfSSL embedded SSL/TLS library is a lightweight SSL library written in ANSI standard C and targeted for embedded and RTOS environments - primarily because of its small size, speed, and feature set. It is commonly used in standard operating...
2.73 MB  
Libraries  -  EuGTK 4.8.9
Makes it easy to develop good- looking, fast, cross-platform programs that run on Linux, OS X, and Windows. Euphoria is a very fast interpreted/compiled language with straight-forward syntax. EuGTK allows programming in a clean, object-oriented...
10.68 MB  
Libraries  -  Linux User Group Library Manager 1.0
The LUG Library Manager is a project to help Linux User Groups start their own library. A LUG library is helpful to the community at large because it increases access to information, and gives everyone the opportunity to become more knowledgeable.
5.35 KB  
Libraries  -  Module::MakefilePL::Parse 0.12
Module::MakefilePL::Parse is a Perl module to parse required modules from Makefile.PL. SYNOPSIS use Module::MakefilePL::Parse; open $fh, Makefile.PL; $parser = Module::MakefilePL::Parse->new( join("", ) ); $info = $parser->required;...
8.19 KB  
Libraries  -  sqlpp 0.06
sqlpp Perl package is a SQL preprocessor. sqlpp is a conventional cpp-alike preprocessor taught to understand SQL ( PgSQL, in particular) syntax specificities. In addition to the standard #define/#ifdef/#else/#endif cohort, provides also...
10.24 KB