• Please, do not forget to enter the SEQUENCE LENGTH (number of residues) as an integer number.  If this value is not entered in the specified text field an ERROR MESSAGE: 'Wrong Sequence Length Format' appears.

• The number of residues (which is needed in order to run the joint prediction) can easily be found in the TMPpred results file. If CoPreTHi is run via the PRED-TMR page, the SEQUENCE LENGTH , as well as the SEQUENCE NAME are automaticaly transfered to the Input Form of the program.

• In order to have the NAME of the SEQUENCE displayed in the results a user should enter a name in the SEQUENCE_NAME text field. The Sequence Name may contain any valid characters (letters or numbers).

• If no parameters are entered for one method, the program returns empty table rows for that method. In the graphical representation a ' "METHOD_NAME" did not predict any transmembrane regions ' label appears. If, for any reason, no data at all are entered then an error message appears in the ERROR text area warning the user that: ' YOU HAVE ENTERED NO PARAMETERS..TRY AGAIN '.

• BE CAREFUL!!! In some of the methods the data format is very strict, so take a careful look in the individual method's data description given below. If the data is not in the correct format an ERROR MESSAGE: 'Nfe :wrong number format in 'METHOD_NAME' method' appears. A general instruction would be to avoid to insert empty lines at the start, end or between the data lines entered to the program.

• To Copy  text, select it (by dragging the mouse with the left button pressed) and press on your keyboard CTRL + C .  To  Paste it just click with the mouse into the desired text area and press  CTRL + V .

The character counter, placed above each method's result, might help to align correctly the copy-pasted text.

DAS method :

The part of the DAS output file that you have to copy and paste in the text area is displayed below in GREEN characters.

12345678901234567890123456789012345(character counter)

Potential transmembrane segments

Start   Stop    Length  ~       Cutoff

56      80      25      ~       1.7
57      79      23      ~       2.2
117     122     6       ~       1.7

Be careful NOT to enter empty lines at the beginning, end or between lines of this text.

• It is very important not to change this format as the Start-Stop values have to be strictly at these positions.
• Otherwise the program will fail to use the DAS method's output.
Go to DAS Input Page
..or to CoPreTHi Input Page

PHD method :

The part of the PHD output file that you have to copy and paste in the text area is displayed below in GREEN characters.

1234567890123456789012345678901234567890123456789012345678901234567890123456789(character counter)

--- PhdTopology REFINEMENT AND TOPOLOGY PREDICTION
                  ....,....1....,....2....,....3....,....4....,....5....,....6
         AA      |MEKDCQDIQQLDSEENDHQLSGDDEHGSHVQDPRIENPHWKGQPLSRPFPQRLCSTFRLS|
         PHD htm |                                                       TTTTT|
 detail:         |                                                            |
         prH htm |000000000000000000000000000000000000000000000000000123456788|
         prL htm |999999999999999999999999999999999999999999999999999876543211|
  other:         |                                                            |
         PHDFhtm |                                                       TTTTT|
         PHDRhtm |                                                         TTT|
         PHDThtm |iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiTTT|
 subset:         |                                                            |
         SUB htm |............................................................|
                  ....,....7....,....8....,....9....,....10...,....11...,....12
         AA      |LLALAFNILLLVVICVVSSQSIQLQEEFRTLKETFSNFSSSTLMEFGALDTLGGSTNAIL|
         PHD htm |TTTTTTTTTTTTTTTTTT                                          |
 detail:         |                                                            |
         prH htm |899999888999988875321000000000000000000000000000000000000000|
         prL htm |100000111000011124678999999999999999999999999999999999999999|
  other:         |                                                            |
         PHDFhtm |TTTTTTTTTTTTTTTTTT                                          |
         PHDRhtm |TTTTTTTTTTTTTTT                                             |
         PHDThtm |TTTTTTTTTTTTTTTooooooooooooooooooooooooooooooooooooooooooooo|
 subset:         |                                                            |
         SUB htm |............................................................|
                  ....,....13...,....14...,....15...,....16...,....17...,....18
         AA      |TSWLAQLEEKQQQLKADHSTLLFHLKHFPMDLRTLTCQLAYFQSNGTECCPVNWVEFGGS|
         PHD htm |                                                            |
 detail:         |                                                            |
         prH htm |000000000000000000000000000000000000000000000000000000000000|
         prL htm |999999999999999999999999999999999999999999999999999999999999|
  other:         |                                                            |
         PHDFhtm |                                                            |
         PHDRhtm |                                                            |
         PHDThtm |oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo|
 subset:         |                                                            |
         SUB htm |............................................................|
                  ....,....19...,....20...,....21...,....22...,....23...,....24
         AA      |CYWFSRDGLTWAEADQYCQLENAHLLVINSREEQDFVVKHRSQFHIWIGLTDRDGSWKWV|
         PHD htm |                                                            |
 detail:         |                                                            |
         prH htm |000000000000000000000000000000000000000000000000000000000000|
         prL htm |999999999999999999999999999999999999999999999999999999999999|
  other:         |                                                            |
         PHDFhtm |                                                            |
         PHDRhtm |                                                            |
         PHDThtm |oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo|
 subset:         |                                                            |
         SUB htm |............................................................|
                  ....,....25...,....26...,....27...,....28...,....29...,....30
         AA      |DGTDYRSNYRNWAFTQPDNWQGHEQGGGEDCAEILSDGHWNDNFCQQVNRWVCEKRRNIT|
         PHD htm |                                                            |
 detail:         |                                                            |
         prH htm |000000000000000000000000000000000000000000000000000000000000|
         prL htm |999999999999999999999999999999999999999999999999999999999999|
  other:         |                                                            |
         PHDFhtm |                                                            |
         PHDRhtm |                                                            |
         PHDThtm |oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo|
 subset:         |                                                            |
         SUB htm |............................................................|
                  ....,....31...,....32...,....33...,....34...,....35...,....36
         AA      |H|
         PHD htm | |
 detail:         | |
         prH htm |0|
         prL htm |9|
  other:         | |
         PHDFhtm | |
         PHDRhtm | |
         PHDThtm |o|
 subset:         | |
         SUB htm |.|
---
--- PhdTopology REFINEMENT AND TOPOLOGY PREDICTION END

Go to PHD Input Page
..or to CoPreTHi Input Page

ISREC method :

The part of the ISREC output file that you have to copy and paste in the text area is displayed below in GREEN characters.

123456789012345678901234567890123456789012345678901234567890123(character counter)

 1) From   59 to   77 (type 1):  length= 19, score=61.00  ** 
      59  LSLLALAFNI LLLVVICVV
    L:  7(36.8%);  A:  2(10.5%);  V:  4(21.1%);  I:  2(10.5%);

• Please, note that there is a space character that should NOT be omitted
Go to ISREC Input Page
..or to CoPreTHi Input Page

TMPred method :

The part of the TMPred output file that you have to copy and paste in the text area is displayed below in GREEN characters.

1234567890123456789012345678901234567890123456789012345(character counter)

-----> STRONGLY prefered model: N-terminus outside

 7 strong transmembrane helices, total score :      11744

# from   to length score orientation

 1   59   77 (19)    2582 o-i

..or..

------> alternative model

 6 strong transmembrane helices, total score :       9862

 # from   to length score orientation

 1   61   78 (18)    2219 i-o

• Be careful NOT to enter empty lines in the begining, end or between lines of this text.
• It is very important not to change this format as the from-to values have to be strictly in these positions.
• Otherwise the program will fail to use the TMPred method's output.
Go to TMpred Input Page
..or to CoPreTHi Input Page

TopPred method :

The part of the TopPred output file that you have to copy and paste in the text area is displayed below in GREEN characters.

123456789012345678901234567890123456(character counter)

  Helix Begin   End   Score Certainity
      1    59    79   2.085 Certain
      2   107   127   0.714 Putative

Go to TopPred2 Input Page
..or to CoPreTHi Input Page

SOSUI method :

To get the part of the SOSUI output that you have to enter in the text area you have to follow the next simple procedure:

1. First, select from the 'View' menu of your browser the option 'source' (the name of the option may differ slightly from browser to browser).
2. Then, select (by draging the mouse with the left button pressed) on the text like the one displayed below in GREEN characters.
3. Copy the text ( CTRL + C) and then paste ( CTRL + V ) it in the appropriate text area of the input form.

123456789012345678901234567890123456(character counter)


<param name="1s" value="58">
<param name="1e" value="80">

• Please, don't forget the '<' and '>' characters.
• The number of the SOSUI parameters should always be a multiple integer of 2
Go to SOSUI Input Page
..or to CoPreTHi Input Page
 
 

PRED-TMR method :

The part of the PRED-TMR output that you have to copy and paste in the appropriate text area is displayed below in GREEN characters.

12345678901234567890(character counter)
     predicted            observed 
#TM  begin  end          begin  end
 1     59    77            59    79

Go to PRED-TMR Input Page
..or to CoPreTHi Input Page   

---

OBSERVED:

Observed transmembrane domains may also be entered.  In this case, an evaluation of the prediction schemes is obtained against the observed data.  This input should follow the SWISS-PROT format, as shown below in GREEN characters:

123456789012345678901234567890123456789012345678901234567890(character counter)

KW   LECTIN; GLYCOPROTEIN; RECEPTOR; ENDOCYTOSIS; TRANSMEMBRANE;
KW   CALCIUM; SIGNAL-ANCHOR; PHOSPHORYLATION.
FT   DOMAIN        1     58       CYTOPLASMIC (POTENTIAL).
FT   TRANSMEM     59     79       SIGNAL-ANCHOR (TYPE-II MEMBRANE PROTEIN).
FT   DOMAIN       80    301       EXTRACELLULAR (POTENTIAL).
FT   DOMAIN      169    295       C-TYPE LECTIN (LONG FORM).
FT   DISULFID    170    181       BY SIMILARITY.
FT   DISULFID    198    293       BY SIMILARITY.
FT   DISULFID    271    285       BY SIMILARITY.

This is also the format to enter the results of any prediction scheme, not mentioned above in the 'CUSTOM METHOD' text area.


---

HTML results

By choosing 'HTML results' the program returns a Graphical representation of the Histogram that Combines the predictions of the above methods, as well as tables with the predictions from individual methods and the segments predicted to be transmembrane by 3 or more methods. Unfortunately, it is not possible to save this page (at least for the moment) unless if you use special software to save the contents of your screen in picture-files.

To take a quick look at a sample Combined Histogram for LECI_MOUSE just click HERE!!!

TEXT results

By choosing 'TEXT results' the program returns the above table contents in Plain Text, so one can easily save them either as an 'HTML' page or in Text Format (by copying and pasting them in a text editor). No graphical representation is returned.

Try to copy and paste data in the Input Form.
For further questions send e-mail to: vprobon@biol.uoa.gr 

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