Example for requesting to return the 1D structure prediction in COLUMN format

Bold face: keyword "return COLUMN format"

Abbreviations: sequence (AA); secondary structure (PSEC) with H=helix, E=strand, or L=rest; relative accessibility (PACC) with o=outside (>15% accessible), and i=inside (<15% accessible); reliability of prediction for secondary structure (RI_SEC) and solvent accessbility (RI_ACC) scaled from 0 (low) to 9 (high).

Input (request of you)

Joe Sequencer, Department of Advanced Protein Research,
National Univeristy, Timbuktu
joe@amino.churn.edu
return COLUMN format   
# 434 cro protein
MQTLSERLKKRRIALKMTQTELATKAGVKQQSIQ

Output (result returned)

• Block with sequence alignment.
• Block with information about prediction method.
• Block with prediction in default format.
• Block with prediction in COLUMN format:

       AA  PSEC PACC    RI_SEC   RI_ACC
       M   L    152     9        3
       Q   L     97     9        2
       T   L     69     8        4
       L   H      0     4        4
       S   H     63     8        4
       E   H     95     9        5
       R   H     89     8        2
       L   H      0     7        2
       K   H    100     9        5
       K   H    100     9        8
       R   H     89     9        2
       R   H     89     9        1
       I   H     82     9        3
       A   H      0     9        2
       L   H      0     9        6
       K   H    100     9        6
       M   H     92     9        3
       T   H     51     9        1
       Q   H      0     9        1
       T   H     69     9        4
       E   H     95     9        4
       L   H      0     9        3
       A   H      0     9        9
       T   H     69     9        5
       K   H    100     9        8
       A   H     51     4        6
       G   L     41     8        4
       V   L     69     9        4
       K   L    100     3        7
       Q   H     97     6        4
       Q   H     71     9        1
       S   H      0     9        7
       I   H      0     9        5