Name: COBALT Components

Author: Yann Darsel

Version: 1.0

Created: 01/2008

Modified: 01/2008

Purpose: These components allows multiple sequences alignments using COBALT - COnstraint-Based ALignment Tool, on a Local or on a Remote machine. The COBALT algorithm is described in Papadopoulos J, Agarwala R, "COBALT: COnstraint-Based ALignment Tool for Multiple Protein Sequences", Bioinformatics. 2007 May 1;23(9):1073-9. Epub 2007 Mar 1.

Requirements: Linux executable for COBALT
Pipeline Pilot 6.0 or later
Sequence Analysis collection

O/S: Windows and Linux

Limitations: none known

Keyword: alignment, COBALT

Contents: Align Sequences (Cobalt).xml, Align Sequences (Cobalt - Remote Machine).xml

Installation:

1. To install, you will need administrator access to the Pipeline Pilot server.
2. Download Linux executable for COBALT from the ftp server indicated in the publication (see above)
3. Install Linux executable for COBALT according to readme instructions onto a Linux Server Machine (can be the Pipeline Pilot server).
4. Unzip the archive.
5. Attempt to use the components in an alignment protocol. Use 'Align Sequences (Cobalt)' component if your Pipeline Pilot server is installed on a Linux Machine. Use 'Align Sequences (Cobalt- Remote Machine)' component if your Pipeline Pilot server is installed on a Windows Machine (A Password or Key File is required in both SSH and SCP components into this subprotocol component).

Contact bioinfo.darsel@gmail.com for more information.