EMBnet Norway

Toolkit Manuals/Reference page

Here, you will find a collection of selected documentation material related to the most commomly employed applications of the node.

EMBOSS/EMBASSY Documentation

• Revised Documentation for Release 6: Alphabetical and view-by-category listing of EMBOSS programs.
• You can find a user-orientated EMBOSS tutorial here, made originally by the MRC Rosalind Franklin Centre for Genomics Research (RFCGR), UK. This is a self-study orientated tutorial. In addition, EMBnet has published the EMBOSS quick reference guide.
• Users moving to EMBOSS from the older GCG package will certainly find this table useful.

Accelrys GCG 11.0

• New command synopsis(pdf) and User Release notes(pdf)
• Accelrys SeqMerge Tutorial(pdf) which effectively replaces the old Fragment Assembly System (Gel* utilities). There is also a guide(pdf) that explains how to import Gel* projects to SeqMerge.

MUMmer/NUCmer/PROmer documentation

• MUMMER on line manual

PERL Documentation

• PERL Quick Guide
• PERL Regular Expressions Quick Guide

PHYLIP Documentation

• A quick guide to the phylogeny inference application PHYLIP

NCBI BLAST Documentation

• NCBI BLAST version 2.2.15 has some important changes in the way you format the databases. Please read here for more information.
• A quick guide published by EMBnet.

BLASTZ Documentation

• BLASTZ alignment tool (proteas.uio.no) for long sequences Readme file.
• 'LAJ' is a tool for manipulating the output from pairwise alignments from blastz. The node offers the applet version of the tool. Information on how to install it in your JAVA-enabled browser can be found here.

UNIX/LINUX Command line Documentation

• A handy UNIX quick quide for a fast lookup of essential UNIX commands.
• A tutorial on how to connect to the command line facilities using PuTTY and Xming from a Windows workstation can be found here. This tutorial replaces previous documentation concerned F-Secure SSH and X-Win32.
• A UNIX/LINUX tutorial in MS PowerPoint and OpenOffice compatible format written by George Magklaras of EMBnet Norway for self-paced study. After a short introduction to the history of UNIX and LINUX, the basic concepts of the 'shell' and 'filesystems' are introduced. This tutorial requires no prior knowledge of UNIX and it contains references to additional documentation for Biologists that need to expand their basic knowledge of UNIX/LINUX .

---