bam2fastq 1.1.0 – Extract Sequences from a BAM file in Fastq format

bam2fastq 1.1.0

:: DESCRIPTION

bam2fastq is a program to extract sequences and qualities from a BAM file.

::DEVELOPER

The Genomic Services Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler
:: DOWNLOAD

 bam2fastq

:: MORE INFORMATION

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

J. Cris Vera

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Perl

:: DOWNLOAD

 TableParser

:: 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

Jiang (River) Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 MitoSeek

:: 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

Ingo Bormann

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX

:: DOWNLOAD

DigitizeIt

:: 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

RNA-eXpress

::REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 RNA-eXpress

:: 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

Cesim ErtenMelih Sözdinler

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Visual Studio 2005 C++

:: DOWNLOAD

 LEB

:: 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.

EDISA Online Version

::DEVELOPER

the Center for Bioinformatics Tübingen (Zentrum für Bioinformatik Tübingen, ZBIT).

:: SCREENSHOTS

EDISA

:: REQUIREMENTS

  • Linux/ WIndows
  • Matlab

:: DOWNLOAD

  EDISA

:: 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

 sff_extract

:: 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

Virtual Biology Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 EmblEx

:: 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

Bergman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

 EcologIE PMCMiner

:: MORE INFORMATION

Citation:

An exploration of mining species interaction data from the ecology literature,
Springate and Bergman 2012 (forthcoming).