AFAWE Automatic functional annotation in a distributed Web Service environment

About This Presentation

Title:

AFAWE Automatic functional annotation in a distributed Web Service environment

Description:

AFAWE. Automatic functional annotation in a distributed Web Service environment ... Platform independent. Web services can be used from all over the world ... – PowerPoint PPT presentation

Number of Views:93

Avg rating:3.0/5.0

Slides: 14

Provided by: PCB81

Category:

more less

Transcript and Presenter's Notes

Title: AFAWE Automatic functional annotation in a distributed Web Service environment

1
AFAWEAutomatic functional annotation in a
distributed Web Service environment

Anika Joecker

2
How to assign functions to genes?
?
3
Problems

Which data is available?
Where to get the up-to-date data?
Where to set the cutoffs?
Which are the true orthologs?
Which descriptions are experimentally verified?
gt Manually comparison of different results
gt No graphical result for many methods yet
gt The whole process is very time-consuming

4
Idea

Automate the comparison of results (by using
artificial intelligence/machine learning
algorithms)
Run as many programs as are available (by using
Web services)
Output
Human readable description (Summary)
Important nomenclatures for gene function (e.g.
EC-number, GO-term, FunCat, KO-term, MapMan bin)
Score and rank the results, highlighting
trustworthy vs. dubious ones

5
Which information will be used?
6
Why use Web services?

Use programs and data remotely through the
internet
No need to install anything, no need to have a
fast computer
Programs and databases are always up-to-date
Platform independent
Web services can be used from all over the world
Many bioinformatics tools are available as Web
services
Faster access to the data

7
Application design
8
Included Web Services/Workflows

RPS-Blast against the CDD database (Riken
university)
InterProScan (EBI)
WUBlast (EBI)
Blastp against a database with experimentally
verified GO terms (MPIZ)
SIFTER pipeline

9
Functional annotation / SIFTER pipeline
10
Web interface
11
Advantages

It is very easy to include more data (Web
Services)
Data is always up-to-date
No need to install the analysis software
No need for much compute power

12
Outlook

AFAWE web interface will become available in
autumn
Implementation and integration of new Web
Services is underway
Using AFAWE for the functional annotation in the
Medicago truncatula project IMGAG and in the
tomato annotation project ITAG

13
Thanks