coevolution webserver

Q:

I have read the article “An integrated system for studying residue coevolution in proteins” and start to use the coevolution webserver http://coevolution.gersteinlab.org/coevolution/. The help page says SCA is one of the coevolution score function, which I can‘t find on the webpage. Could you please tell me what is wrong?

A:
SCA is only available in the version for download, but not at the Web site anymore since it sometimes ran for an extremely long time. If you want to use the SCA method, you can use the download version or the latest SCA method by the Ranganathan group, which I think is better than the version we implemented.

Questions re tool for coevolution analysis

Q:
We are interested in
adding a link to your tool on the website. I have been playing around with
the tool but have been having some difficulty. I loaded the example, ran the
analysis and downloaded the results with no problem. Then, I tried to use
the data from the example to re-run the analysis by uploading the PF01036
fasta file (as an MSA) and listing BACR_HALSA as the reference sequence. I
did not load the tree data or the structure data. I submitted the request
and received the following error:

The coevolution analysis task that you submitted at 2013-09-11 11:35:07.0
could not be completed.

Error message:Not enough sequences.

In order to justify the addition of the link to the website, we need to make
sure that the web interface is simple and easy to use. Can you help me
understand what the problem might be (clearly I have enough sequences since
the example runs without any issues)? Also, can you explain to me the link
between the 1C3W reference structure and the sequence data?

Any help you can give would be greatly appreciated.

A:
The error message is due to an internal check of the system. Since
coevolution analysis requires a good number of sequences to give
reliable statistics, there is a minimum threshold of the number of
sequences after the filtering step. When the example is loaded, I think
some of the filtering settings are made so that it can pass the minimum
threshold. When one manually uploads the MSA, the default settings could
be different.

You may try changing the setting for the minimum number of
sequences in the "Advanced options" section (which is by default hidden)
and rerun. Let me know if you still get any error message.

Completion of job on coevolution server

Q:

we are trying to find the co-evolving positions in a protein family of interest. I had submitted a job on the co-evolution server several days back, but I have not received a response yet. Could you please let me know the estimated time of completion of my job?

A:
There was a long queue of pending tasks, and one of had been stuck in the queue for some time. I have removed it to let the others run. Please see if you can get your results within a day. If not, please let me know and I will check the system again.