[Bio-Linux] new packages on Bio-Linux - taverna, estscan and prot4est

[Bela Tiwari]

Hello,

This is an email to alert you to new Bio-Linux packages available:


1) Taverna

Taverna is a graphical interface allowing you to harness the many bioinformatics functions being offered as web services to create customised pipelines to accomplish tasks from the simple to the complex. Example workflows come with the program to help you get a feel for what is possible. The first time a user runs taverna on Bio-Linux, they are offered the opportunity to copy the examples that come with taverna into their home directory. These example workflow files are saved to a folder called tavernaExamples. Some of the examples are rather complex, but some simpler ones which are easier to understand are provided such as:

FetchPDBFlatFile.xml   (within the libraries subfolder)
blast-compare-retry.xml (under the WBSWorkflows subfolder)

or perhaps the best one to start out with:

FetchDailyDilbertComic.xml    (within the tavernaExamples folder itself)

Once installed, taverna can be started by typing "taverna" on the command line, or by choosing the taverna option in the graphical bioinformatics menu.


2) estscan

ESTScan is a commane line program that can detect coding regions in DNA seqeunces, even if they are of low quality. It will also try to detect and correct sequence errors that lead to frameshifts. ESTScan uses a Markov model to represent the bias in hexanucleotide use found in coding regions relative to non-coding regions. 

After installation, ESTScan can be started on Bio-Linux by typing "estscan" on the command line.


3) prot4est

This program takes expressed sequence tags and translates them into putative peptide sequences. It makes use of the ESTScan program and can optionally use the decode program also if that is available on the machine. Please note that the User Guide provided with this package is currently out of date. We will add the new version when it becomes available. The important change relevant to Bio-Linux users is that you do not need to do any additional configuration or installation after installing the bio-linux-prot4est package unless you wish to make use of decoder, which is a licensed piece of software.


As with all new packages added to the Bio-Linux package listing, these packages will not get installed on your machine automatically. One way to install them is through the synaptic interface. Information on how to do that can be found through the following link:

http://envgen.nox.ac.uk/envgen/software/archives/000503.html#Synaptic 



cheers

Bela

*************************
Dr. Bela Tiwari
Lead Bioinformatician
NERC Environmental 
Bioinformatics Centre

CEH Oxford
Mansfield Road
Oxford, OX1 3SR
01865 281975

*************************


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