Staden 2.0.0b11 – DNA Sequence Assembly , Editing and Analysis

Staden 2.0.0b11

:: DESCRIPTION

Staden is a fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) .

::DEVELOPER

Staden Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

Staden

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jul 15;26(14):1699-703. doi: 10.1093/bioinformatics/btq268. Epub 2010 May 30.
Gap5–editing the billion fragment sequence assembly.
Bonfield JK1, Whitwham A.

Rodger Staden, David P. Judge and James K. Bonfield.
Analysing Sequences Using the Staden Package and EMBOSS.
Introduction to Bioinformatics. A Theoretical and Practical Approach. Eds. Stephen A. Krawetz and David D. Womble. Human Press Inc., Totawa, NJ 07512 (2003)

STAMP 1.1 – Microsatellite Marker Design Extension for the Staden package

STAMP 1.1

:: DESCRIPTION

STAMP is a Staden package extension for automating microsatellite marker design. It integrates the de novo repeat identification program Phobos by Christoph Mayer and PRIMER3 into Pregap and Gap4. It allows tagging repeats for masking them out for assembly (Pregap), finding repeats in assembled Gap4 databases, automatic primer design flanking marked repeats and multiplex primer design.

::DEVELOPER

Christoph Mayer

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • Staden

:: DOWNLOAD

 STAMP

:: MORE INFORMATION

Citation

Kraemer, L., Beszteri, B., Gäbler-Schwarz, S., Held, C., Leese, F., Mayer, C., Pöhlmann, K. & Frickenhaus, S (2009)
STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design.
BMC Bioinformatics 10:41.

Staden io_lib 1.13.10 – C library of file reading and writing code to provide a general purpose Trace file

Staden io_lib 1.13.10

:: DESCRIPTION

Staden io_lib  is a library of file reading and writing code to provide a general purpose trace file (and Experiment File) reading interface.

::DEVELOPER

Staden Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • C Compiler

:: DOWNLOAD

 Staden io_lib

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jun 14. pii: btu390.
The Scramble Conversion Tool.
Bonfield JK.