RNALI

Summary

RNALI is a client/server Java application that allows to:
  1. Align a new rRNA sequence relatively to a database of aligned rRNA sequences.
  2. Position the new sequence in the taxonomical classification of organisms represented in the database.
  3. Select representative sequences from the database.
  4. Extract the new sequence aligned with chosen representative sequences.
The database of prealigned rRNAs accessed from RNALI is that from the rRNAWWW server at Antwerp. The taxonomical classification of associated organisms is that from the NCBI.

Installation

RNALI is presently available as a Java aplication for UNIX workstations only. The directory containing the whole distribution can be reached at URL:

<ftp://pbil.univ-lyon1.fr/pub/rnali>

All the Java classes required to run RNALI are stored into a java archive file named rnali.jar. This archive does not need to be expanded to install RNALI. Retrieve this file using the binary mode of your FTP client and save it in the directory where you want to have the program located. You have also to get the Help file to be able to access the on-line help when running RNALI. Note that this file need to be retrieved using the ascii mode of your client.

To install the program, you must also retrieve the C shell file rnali.csh and then edit it by replacing the string ~/rnali by the path leading to the directory containing the files Help and rnali.jar. By default RNALI uses 4 Mbytes of memory, if it needs more memory you have to indicate it in the file rnali.csh by relacing the value 4 by a greater value.

Start

To start the program, go to the directory where thernali.csh file is stored and type rnali.csh. Another possibility is to copy or move this shell file to one of the directories that are listed in the PATH environment variable.

Contact

If you have questions or comments about RNALI, please contact:

Said Abdeddaim
Département d'Informatique de Rouen
Faculté des Sciences et Techniques
Université de Rouen
F-76821 Mont-Saint-Aignan Cedex

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