The PSIPRED Server Help Page
Type your AMINO ACID sequence here. Please do not try to enter a nucleic acid sequence.
We recommend that you enter your sequence as a plain single-letter string like this:
Alternatively, you can enter your sequence in FASTA format, but the description text will be ignored by the server.
Note that there is an upper limit to
the length of sequences which can be submitted. For mGenTHREADER that
limit is 1000 residues. For the other methods, the
limit is 1500 residues. If your sequence is longer than this, try
into likely domains before submitting it. Our DomPred server can help you in doing this.
Choose Prediction Method
Select which method you wish to use. See the PSIPRED home page for more details on the different methods (and references).
To reduce the false positive rate of fold recognition methods,
particularly when applied to
long sequences, it is important that biased regions of the target
sequence are filtered out
before the prediction is carried out. The PSIPRED server uses the PFILT
program to perform the masking and has 3 filtering options, which will
filter out low complexity regions, likely transmembrane segments and
coiled-coil regions. The
default setting is for just low-complexity regions of the sequence to
be masked out. Regions
which are masked out will be replaced with 'X' (unknown) residues.
Obviously, if you filter out transmembrane helices and then try to use MEMSAT2 to predict
the transmembrane topology, you will not get sensible results. For GenTHREADER
and mGenTHREADER we recommend turning on all filtering if you are expecting
matches to globular proteins.
Enter your e-mail address here. Results will be returned as soon as
they are available - usually within 20 minutes, though sometimes longer
depending on the server load.
Bear in mind that if you enter an incorrect e-mail address, there is no
way the server can contact you! Also watch out that your anti-spam
rejecting the messages from our server.
This field should be ignored if you are accessing the server from
an academic site (i.e. a University).
If you are a commercial user who has a current license to use the
PSIPRED server then you should enter your password here. Please contact
us if your password does not work for some reason.
Note that if your e-mail address is commercial - e.g. ends .com or
.co.uk - then you must enter your PSIPRED password in order to use the
server. This applies even if you are an academic user who is using a
private e-mail account. PSIPRED passwords are only granted to licensed
users or commercial collaborators.
Please note that you cannot use free e-mail addresses such as
hotmail.com or yahoo.co.uk to access the PSIPRED server under any
circumstances. It is not possible to make exceptions to this, so please
do not ask us about it.
Short name for sequence
Use this field to assign a short memorable name to your prediction
job. This is useful so that you can identify particular jobs in your
mailbox. This is particularly important because PSIPRED will not
necessarily return your results in the order you submitted them!
Generally speaking, shorter jobs will be returned first.
The name you specify will be included in the subject line of the e-mail
messages sent to you from the server. For example, here is the message
header for a job called "MySeq":
Date: Fri, 14 Jan 2002 14:55:39 GMT
Subject: MySeq PSIPRED Results
PSIPRED PREDICTION RESULTS
... results ...