Version

Version 6.3.1 is installed in hippu.csc.fi. ( ChangeLog for EMBOSS 6.3.1)

Version 6.3.1 is installed in vuori.csc.fi

Version 6.3.1 is installed in murska.csc.fi.

Description

EMBOSS (European Molecular Biology Open Software Suite) package contains over 200 programs for sequence analysis. Examples of application areas of EMBOSS tools are given below.

• Sequence alignment
• Phylogeny
• Hidden Markow models
• Rapid database searching with sequence patterns
• Protein motif identification, including domain analysis
• EST analysis
• Nucleotide sequence pattern analysis, for example to identify CpG islands.
• Simple and species-specific repeat identification
• Codon usage analysis for small genomes
• Rapid identification of sequence patterns in large scale sequence sets.
• Presentation tools for publication
• RNA secondary structure prediction

Usage

Graphical EMBOSS interfaces

Most EMBOSS progams can be used via the Embster server. To use Embster you need a user account at CSC.

• Open Embster client
  

EMBOSS in Hippu

To make EMBOSS programs available in Hippu, give command:

module load emboss

After this you can start any of the EMBOSS programs by typing its name. For example:

wossname

If you can open an X-term connection from  hippu.csc.fi  to your local machine, you can use the graphical Jemboss user interface. In addition to the EMBOSS programs, Jemboss includes Jalview and Jemboss sequence alignment editorts and Jemboss DNA Editor. You can start Jemboss with commands:

module load emboss
jemboss

EMBOSS in Vuori and Murska

To make EMBOSS programs available in Vuori or Murska, give command:

module load emboss

After this you can start any of the EMBOSS programs by typing its name. For example:

wossname

EMBOSS databases in Hippu

The databases listed bellow are indexed for EMBOSS in Hippu. This means that in Hippu and Scientist's Interface you can access sequences from these databases using the USA sequence address: database:access_code. For example:

infoseq swiss:CASA1_HUMAN

Help

• Homepage of EMBOSS project 
• EMBOSS programs sorted alphabetically
• EMBOSS programs sorted by function
• EMBASSY programs (HMMER, MEME, MSE, Phylip, sim4, TOPO, Vienna)

• EMBOSS Quick Guide

• EMBOSS Administrators Guide

Tutorial

• Getting started with EMBOSS -tutorial
  
• Sekvenssianalyysiopas