Introduction

The Computational Biology Division (CBIO) at UCT is willing to play a role in providing bioinformatics
support to researchers at the university. We can provide advice on bioinformatics protocols, methods
and tools to use, as well as some basic training. We have a small computer cluster at CBIO and ICTS
have a high performance computing cluster, both of which have several bioinformatics applications
and pipelines installed. Members of UCT can apply for access to the ICTS cluster and they provide basic
training on how to use the cluster and help with installation and use of new tools.
Although our team has a wide range of skills, bioinformatics is a large area. If a support request is
outside of our area of expertise, we’ll do our best to point you in the right direction as we have
excellent relations with other South African bioinformatics groups. Like any service, bioinformatics
services should be paid for. CBIO does not receive any UCT funding to provide support so there usually
needs to be a quid pro quo for the support offered. We recognise that there are a wide range of needs
and we shall endeavour to be as flexible as possible. We emphasise the need to talk to us as early as
possible in a research project. Bioinformatics is a large component of many projects and must be
planned from the beginning both with respect to scientific method and available resources.

Blast2GO Local Web Service

Blast2GO is an ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data. Running Blast2GO is easy, just follow these instructions.

 

Although the software runs on your computer it needs to connect to an external database and web service to function properly. The default settings are set to the database and web service hosted at Blast2GO. If you have a slow connection to this database it can affect the speed of mapping and annotation. An alternative is to have a local database installed to allow faster access. We have a local database and web service installed at CBIO and find that their is a significant improvement in the annotation and mapping process. Our services is publicly available so please feel free to use it!

 

The database settings can be changed within the Blast2GO application or within the "Blast2GO properties file" stored on your system. The settings for the web service can only be done in the "Blast2GO properties file".

 

The following settings need to be changed in the "Blast2GO properties file":

 

---------------------------------------------------------------------
// Conectivity to WebServices
Webservice.url=http://omweso.cbio.uct.ac.za:8180/b2gws_axis2

 

// GO and B2G-Mapping Database
Dbacces.dbhost=omweso.cbio.uct.ac.za
Dbacces.dbname=b2g
Dbacces.dbuser=blast2go
Dbacces.dbpasswd=blast4itza
---------------------------------------------------------------------

 

In Linux the property file will be in "/home/user/blast2go/blast2go.properties" and Windows in e.g. "c:\\Documents and Settings\user\blast2go\blast2go.properties"

 

Please consult the Blast2GO manual for detail instructions on how to use and configure the application.

 

Our local Blast2GO database was updated on 04/01/2011

 


 

 

CBIO tools