OMICtools can help a) experimental researchers/clinicians find appropriate tools for their needs b) developers to stay up to date and to avoid redundancy c) funding agencies to ensure that the submitted projects are high value-added. Do you want help us to improve OMICtools? Details here.

Publication: OMICtools: an informative directory for multi-omic data analysis
Vincent J. Henry; Anita E. Bandrowski; Anne-Sophie Pepin; Bruno J. Gonzalez; Arnaud Desfeux
Database 2014; doi: 10.1093/database/bau069

It's the-state-of-the-art algorithm for the multiple network alignment problem. Fast, Scalable, and Accurate!
Posted by Heidi on Aug 13, 2014
Functional annotation enrichment analysis is a powerful first step to understanding an interesting list of genes or gene products.

When I do it, I want the tool to have at least these features:
1) Up-to-date GO annotation data, and support as many other databases as possible;
2) Recognizing multiple types of gene or protein identifier, and do the conversion in the background;
3) Comprehensive filter to reduce or organize the hierarchically inter-related terms to minimize redundancy;
4) Good visualization;
5) Fast.

Of about a dozen different tools I have tried, gProfiler is the only one I found satisfying all. Plus, it has an API in R, which is a life-saver.

One thing that could be improved is to include annotation term clustering according to their semantic or functional similarity (you can try DAVID for this).
Posted by xtYaoNYU on Aug 12, 2014
My new favourite!
Posted by John L on Aug 10, 2014
you need to download the UNAFold software separately from
Posted by J on Aug 05, 2014
Let's try!
Posted by landiebuku on Aug 04, 2014
Nice package
Posted by Xiaou L. on Aug 01, 2014
NGS-QC Generator
The major characteristics of this approach is its universality; i.e. its capacity of assessing QC descriptors for any kind of ChIP-seq and enrichment-related datasets. In fact all other currently available methods require either the use of peak callers for sites annotations (which require different conditions when treating broad or sharp profiles) or they are mainly designed for sharp enrichment patterns. Importantly, the NGS-QC Generator tool has been used for assessing QC indicators for more than 7000 publicly available datasets and is expected to cover all available datasets in a close future. Such QC indicators are available through the dedicated website
Posted by marco A. Mendoza on Jul 31, 2014
miRecords seems to be down; I can't access the site from the link.
Posted by Eric Dawson on Aug 19, 2014
plz send me the step wise method how to use GOrilla tool becoz I tried many times but error occured..
Posted by divya on Aug 09, 2014
P-MITE database is not accessible. Can someone help to fix it? Thanks.
Posted by Users on Aug 08, 2014
According to RONN developers, the server has been taken down for an upgrade and they are working as quickly as they can to get it back online.
Users may direct their queries to ronn[at][dot]uk in the meantime and they will set them up with local copies of the predictor if they require it.
Posted by Vincent Henry on Aug 07, 2014
Whenever I want to run this server I can't. Rather it is showing this message "An Error Occurred
500 Can't connect to (connect: No route to host)" But i use this server few days ago.
Posted by Urmee on Aug 05, 2014
Web server still not opening on 20140805. Please fix as I have a lecture and tutorial coming up using Metaboanalyst! :)
Posted by James Broadbent on Aug 05, 2014
I want to know in which software these tools are developed?
Posted by Aneeqa Iftikhar on Aug 04, 2014