<p>Hello everyone! This is my first time posting here so I hope I am doing this the right way.</p>

<p>I&#39;m a student in bioinformatics in Qu&eacute;bec, Canada and I just started a summer project with my teacher. I have to predict disordered proteins from a database containing a lot of sequences. I don&#39;t know if any of you is familiar with this process but I&#39;ll ask anyway.</p>

<p>I&#39;ll use DISOPRED3 for the prediction. The problem is that the results I get are not the same on my personal computer as those I get from the server itself. Before using my scripts to predict with all the files I have, I would like to have the same results as the server. I use UniRef90 (like they do) and I installed the last version of the program. What could be different and cause the small differences? I already sent an email asking what they are using but they didn&#39;t respond yet.</p>

<p>Thank you, any help will be appreciated!</p>

<p>If you read the FAQ at the psipred download page (<a href="http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/">http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/</a>), you get:</p>

<pre>
&quot;2. The next most common question we get regards getting different predictions from our PSIPRED web server from those you get on your own system. There are many reasons why this might occur, but the most obvious one is that we are using a
​different sequence data bank to the one you are using. Because modern secondary structure prediction methods are based on</pre>

<pre>
analysing multiple sequence alignments, if your data bank includes some extra sequences or misses out some sequences compared
to our local data bank then you might get a slightly different prediction. Hopefully the differences will be small, but
they can be quite significant if the alignment only includes a few sequences. So, if our server can find say just 5
homologous sequences and your system finds 20 homologous sequences to align, then the predictions may be very different
indeed. That&#39;s just the reality of analysing evolutionary information. If the alignments are different, then the predicted
secondary structure will probably be different.

It&#39;s also possible that we are running a slightly older version of PSIPRED. Oddly enough we don&#39;t update our servers immediately
after releasing a new version of PSIPRED as we need to do internal testing first. So, check that you are running the exact
same version of PSIPRED as our server is currently running. Even so, it&#39;s likely that the real problem is going to be down
to differences in the data banks and alignments that are produced.&quot;</pre>

<p>Also, I am no expert with this software but some structure modelling software are not always deterministic and have a constant seed parameter for debugging purpose. Others (like Rosetta Antibody) are wonderful but will never run or even compile correctly on your laptop.</p>
