bam2fastq 1.1.0
:: DESCRIPTION
bam2fastq is a program to extract sequences and qualities from a BAM file.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux
- C++ Compiler
:: DOWNLOAD
:: MORE INFORMATION
Tag: Extract
TableParser – Extract Sequences from Tab-delimited Assembly Alignment Files
TableParser
:: DESCRIPTION
TableParser: Simple tool for extracting sequences from tab-delimited assembly alignment files (e.g. SimAssembly and AceParser output). Parses out contigs, singletons, and assembled reads into separate files.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Windows / Linux / MacOsX
- Perl
:: DOWNLOAD
:: MORE INFORMATION
MitoSeek 1.3 – Extract Mitochondrial Genome information from Exome Sequencing data
MitoSeek 1.3
:: DESCRIPTION
MitoSeek is an open-source software tool to reliably and easily extract mitochondrial genome information from exome sequencing data. MitoSeek evaluates mitochondrial genome alignment quality, estimates relative mitochondrial copy numbers, and detects heteroplasmy, somatic mutation, and structural variance of the mitochondrial genome.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux
- Perl
:: DOWNLOAD
:: MORE INFORMATION
Citation
Yan Guo, Jiang Li, Yu Shyr, David C. Samuels.
MitoSeek: Extracting Mitochondria Information and Performing High Throughput Mitochondria Sequencing Analysis.
Bioinformatics (2013) 29 (9): 1210-1211
DigitizeIt 2.0 – Extract Data Values from Graphs
DigitizeIt 2.0
:: DESCRIPTION
DigitizeIt digitizer software replaces a digitizer tablet. Sometimes it is necessary to extract data values from graphs, e.g. in most scientific publications only plots but no data values are published. DigitizeIt makes it easy to actually get back numbers from such a plot! This is a three step process: a) import the graph from a file or copy it over the clipboard, b) define the axes system, c) digitize it automatically or manually. Data values can then be saved in ASCII format or copy & pasted directly into any other application, e.g. MS Excel or Microcal Origin.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
- Windows / Linux / MacOSX
:: DOWNLOAD
:: MORE INFORMATION
RNA-eXpress 1.4.3 – Extract & Annotate Transcripts from Next Generation RNA sequencing data
RNA-eXpress 1.4.3
:: DESCRIPTION
RNA-eXpress was designed as a user friendly solution to extract and annotate biologically important transcripts from next generation RNA sequencing data. This approach complements existing gene annotation databases by ensuring all transcripts present in the sample are considered for further analysis.
::DEVELOPER
Centre for Innate Immunity and Infectious Diseases, Monash Institute of Medical Research, Monash University
:: SCREENSHOTS
::REQUIREMENTS
- Windows/Linux/MacOsX
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Mar 15;29(6):810-2. doi: 10.1093/bioinformatics/btt034. Epub 2013 Feb 8.
RNA-eXpress annotates novel transcript features in RNA-seq data.
Forster SC, Finkel AM, Gould JA, Hertzog PJ.
LEB – Localize and Extract Biclusters
LEB
:: DESCRIPTION
LEB is a software of biclustering gene expression data, based on Localize-and-Extract Biclusters
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Windows
- Visual Studio 2005 C++
:: DOWNLOAD
:: MORE INFORMATION
Citation
“Biclustering Expression Data Based on Expanding Localized Substructures” ,
C. Erten, M. Sozdinler,
Proc. of Int. Conf. on Bioinformatics and Computational Biology (BICOB 09).
EDISA 1.0 – Extracting Biclusters from multiple Time-series of Gene Expression Profiles
EDISA 1.0
:: DESCRIPTION
EDISA (Extended Dimension Iterative Signature Algorithm) is a novel probabilistic clustering approach for 3D gene-condition-time datasets. Based on mathematical definitions of gene expression modules, the EDISA samples initial modules from the dataset which are then refined by removing genes and conditions until they comply with the module definition. A subsequent extension step ensures gene and condition maximality. We applied the algorithm to a synthetic dataset and were able to successfully recover the implanted modules over a range of background noise intensities.
::DEVELOPER
the Center for Bioinformatics Tübingen (Zentrum für Bioinformatik Tübingen, ZBIT).
:: SCREENSHOTS
:: REQUIREMENTS
- Linux/ WIndows
- Matlab
:: DOWNLOAD
:: MORE INFORMATION
Citation
Jochen Supper, Martin Strauch, Dierk Wanke, Klaus Harter, Andreas Zell:
EDISA: extracting biclusters from multiple time-series of gene expression profiles
BMC Bioinformatics 2007, 8:334
sff_extract 0.3.0 – Extract the reads from the sff files into Fasta / xml/ caf file
sff_extract 0.3.0
:: DESCRIPTION
sff_extract extracts the reads from the sff files and stores them into fasta and xml or caf text files. 454 sequence reads are usually stored in sff files. In these files the information about the reads is stored: sequence, quality and quality and adapter clips.
::DEVELOPER
Jose Blanca and Bastien Chevreux @ Bioinformatics at COMAV
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux / Windows / MacOsX
- Python
:: DOWNLOAD
:: MORE INFORMATION
EmblEx 20121203 – Parse and Extract data from EMBL entries to various formats
EmblEx 20121203
:: DESCRIPTION
EmblEx (EMBL Extractor) is a software for molecular biologists and bioinformaticians. It consists of a series of perl scripts and makes use of a MySQL database. Using EmblEx is through a graphical interface within a web browser or through the command line under linux or windows.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
EcologIE PMCMiner 0.1 – Extract Information about Species Interactions from the Ecological Literature
EcologIE PMCMiner 0.1
:: DESCRIPTION
EcologIE PMCMiner is a set of tools for extracting putative multispecies interaction data from articles in the Pubmed Open Access Subset.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux / Windows / MacOsX
- Python
:: DOWNLOAD
:: MORE INFORMATION
Citation:
An exploration of mining species interaction data from the ecology literature,
Springate and Bergman 2012 (forthcoming).