Example for requesting prediction-based threading (fold recognition)

Threading based on PHD predictions of secondary structure and accessibility

Joe Sequencer, Department of Advanced Protein Research,
National Univeristy, Timbuktu 
joe@amino.churn.edu
prediction-based threading
# incredulase from paracoccus dementiae, translated from cDNA
KELVLALYDYQEKSPREVTMKKGDILTLLNSTNKD
WWKVEVNDRQGFVPAAYVKKLD

Threading based on your prediction of secondary structure and accessibility

Bold face: keyword "prediction-based threading"

Effect: alignments with possible remote homologues (<25% sequence identity) are returned

Joe Sequencer, Department of Advanced Protein Research,
National Univeristy, Timbuktu 
joe@amino.churn.edu
prediction-based threading
# COLUMN format , incredulase from paracoccus dementiae, translated from cDNA
     AA  PSEC  PACC   RI_SEC   RI_ACC
     M   L    o     9        3
     Q   L    o     9        2
     T   L    o     8        4
     L   H    i     4        4
     S   H    o     8        4
     E   H    o     9        5
     R   H    o     8        2
     L   H    i     7        2
     K   H    o     9        5
     K   H    o     9        8
     R   H    o     9        2
     R   H    o     9        1
     I   H    o     9        3
     A   H    i     9        2
     L   H    i     9        6
     K   H    o     9        6
     M   H    o     9        3
     T   H    o     9        1
     Q   H    i     9        1
     T   H    o     9        4
     E   H    o     9        4
     L   H    i     9        3
     A   H    i     9        9
     T   H    o     9        5
     K   H    o     9        8
     A   H    o     4        6
     G   L    o     8        4
     V   L    o     9        4
     K   L    o     3        7
     Q   H    o     6        4
     Q   H    o     9        1
     S   H    i     9        7
     I   H    i     9        5

Compulsory information: (1) sequence (AA) in one-letter code; (2) secondary structure (PSEC) in either of the states H=helix, E=strand, or L=rest; (3) relative accessibility (PACC) in the two states o=outside (>15% solvent accessible), or i=inside (<15% solvent accessible).

Optional: (1) reliability, or strength for secondary structure (RI_SEC) scaled from 0 (low) to 9 (high); (2) reliability, or strength for relative accessibility (RI_ACC) scaled from 0 (low) to 9 (high).