[Bio-Linux] Bio-Linux package for prank: multiple alignment software

[Bela Tiwari]

Hello

The new multiple alignment software "prank" is now packaged for Bio-Linux. Thanks to Nick Mann for recommending this software.

The web page for this software is:

http://www.ebi.ac.uk/goldman/prank/

To quote from the abstract of their paper:

"We describe a modification of the traditional alignment algorithm that can distinguish insertion from deletion and avoid repeated penalization of insertions and illustrate this method with a pair hidden Markov model that uses an evolutionary scoring function. In comparison with a traditional progressive alignment method, our algorithm infers a greater number of insertion events and creates gaps that are phylogenetically consistent but spatially less concentrated. Our results suggest that some insertion/deletion "hot spots" may actually be artifacts of traditional alignment algorithms."

Reference: Loytynoja A, Goldman N. 2005   An algorithm for progressive multiple alignment of sequences with insertions. Proc Natl Acad Sci U S A.  Jul 26;102(30):10557-62. 	
   

Please note that prank is still under development and the authors note on their website that there may be bugs and there is currently no error checking.  We are on their mailing list and will edeavor to update the bio-linux package whenever we receive alerts from the developers.


Some sample instructions for how to run the software can be found in the README file at /usr/local/bioinf/prank/prank/README or on the website given above.

The bio-linux-prank package can be installed using Synaptic. This software will not be installed automatically although it will be kept updated after it is initially installed. Some information about how to do this can be found at:

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

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


This e-mail and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. Any views or opinions expressed are those of the author and do not represent the views of NERC unless otherwise explicitly stated. The information contained in this e-mail may be subject to public disclosure under the Freedom of Information Act 2000. Unless the information is legally exempt from disclosure, the confidentiality of this e-mail and your reply cannot be guaranteed.