| METHOD about: | ../../doc/explain_methods.html#PX_about_samt99_sec |
| METHOD url: | SAM-T99sec |
| METHOD quote: | K Karplus, C Barrett, and R Hughey:: Hidden Markov Models for Detecting Remote Protein Homologies, Bioinformatics, 14, 846-856, 1998 |
| TYPE : | sec |
| NPROT : | 204 |
| NWEEKS : | 63 |
| AVE_Q3 : | 77.3 |
| AVE_SOV: | 74.9 |
| NOTE 1 : | here ALL results obtained for samt99_sec are given, i.e. NOT those for a common subset! |
| NOTE 2 : | all proteins evaluated had no SIGNIFICANT sequence identity to any protein of previously known structure! |
| type | date | sots | id | Q3 | Q3H%o | Q3H%p | Q3E%o | Q3E%p | Q3L%o | Q3L%p | sov | sovH | sovE | sovL | BAD | info | infoO | infoP | corrH | corrE | corrL | class | contDH | contDE |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| sec | 2008_04_09 | dssp | psum | 77.3 | 86 | 80 | 63 | 74 | 74 | 74 | 74.8 | 82.9 | 74.6 | 68.8 | 3.0 | 0.38 | 0.38 | 0.37 | 0.71 | 0.62 | 0.58 | 8431.3 | 7.3 | 6.9 |
| sec | 2008_04_09 | dssp | sig | 10.6 | 33 | 31 | 42 | 49 | 18 | 17 | 15.0 | 21.5 | 27.9 | 19.5 | 5.1 | 0.17 | 0.18 | 0.18 | 0.24 | 0.29 | 0.20 | 8367.6 | 7.0 | 7.8 |
| sec | 2008_04_09 | dssp | errsig | 0.74 | 2 | 2 | 2 | 3 | 1 | 1 | 1.0 | 1.5 | 1.9 | 1.3 | 0.35 | 0.01 | 0.01 | 0.01 | 0.01 | 0.02 | 0.01 | 585.8 | 0.49 | 0.54 |
| Type | Method | Month | Nprot | Average Q3 for month | File with details for month |
|---|---|---|---|---|---|
| sec | samt99_sec | ALL | 204 | 77.3 | |
| sec | samt99_sec | 2001_04 | 1 | 78.2 | old/2001_04_samt99_sec.html |
| sec | samt99_sec | 2003_07 | 5 | 81.8 | old/2003_07_samt99_sec.html |
| sec | samt99_sec | 2003_08 | 5 | 78.0 | old/2003_08_samt99_sec.html |
| sec | samt99_sec | 2003_11 | 22 | 76.1 | old/2003_11_samt99_sec.html |
| sec | samt99_sec | 2003_12 | 18 | 79.8 | old/2003_12_samt99_sec.html |
| sec | samt99_sec | 2004_01 | 12 | 74.7 | old/2004_01_samt99_sec.html |
| sec | samt99_sec | 2004_02 | 19 | 76.1 | old/2004_02_samt99_sec.html |
| sec | samt99_sec | 2004_03 | 13 | 77.7 | old/2004_03_samt99_sec.html |
| sec | samt99_sec | 2004_04 | 11 | 82.3 | old/2004_04_samt99_sec.html |
| sec | samt99_sec | 2004_05 | 6 | 77.9 | old/2004_05_samt99_sec.html |
| sec | samt99_sec | 2004_06 | 7 | 77.9 | old/2004_06_samt99_sec.html |
| sec | samt99_sec | 2004_07 | 10 | 79.2 | old/2004_07_samt99_sec.html |
| sec | samt99_sec | 2004_08 | 16 | 81.3 | old/2004_08_samt99_sec.html |
| sec | samt99_sec | 2004_09 | 12 | 76.4 | old/2004_09_samt99_sec.html |
| sec | samt99_sec | 2004_10 | 10 | 78.5 | old/2004_10_samt99_sec.html |
| sec | samt99_sec | 2004_11 | 6 | 71.7 | old/2004_11_samt99_sec.html |
| sec | samt99_sec | 2004_12 | 1 | 69.7 | old/2004_12_samt99_sec.html |
| sec | samt99_sec | 2005_02 | 1 | 53.2 | old/2005_02_samt99_sec.html |
| sec | samt99_sec | 2005_03 | 18 | 78.6 | old/2005_03_samt99_sec.html |
| sec | samt99_sec | 2005_04 | 3 | 67.0 | old/2005_04_samt99_sec.html |
| sec | samt99_sec | 2005_05 | 7 | 71.1 | old/2005_05_samt99_sec.html |
| sec | samt99_sec | 2005_06 | 4 | 78.4 | old/2005_06_samt99_sec.html |
| sec | samt99_sec | 2005_07 | 14 | 76.4 | old/2005_07_samt99_sec.html |
| sec | samt99_sec | 2005_08 | 3 | 70.8 | old/2005_08_samt99_sec.html |
| sec | samt99_sec | ALL | 204 | 77.3 |
| psum | percentage over all proteins |
| sig | standard deviation |
| errsig | significant difference (to distinguish between two methods) |
| type | prediction type |
| date | date when added [yyyy_mm_dd] |
| sots | standard of truth |
| id | identifier of protein |
| Q3 | three-state per-residue accuracy (percentage of correctly predicted residues) |
| Q3H%o | correctly predicted helix residues (percentage of helix observed) |
| Q3H%p | correctly predicted helix residues (percentage of helix predicted) |
| Q3E%o | correctly predicted strand residues (percentage of helix observed) |
| Q3E%p | correctly predicted strand residues (percentage of helix predicted) |
| Q3L%o | correctly predicted loop residues (percentage of helix observed) |
| Q3L%p | correctly predicted loop residues (percentage of helix predicted) |
| sov | per segment accuracy (three states) |
| sovH | per segment accuracy for helix residues |
| sovE | per segment accuracy for strand residues |
| sovL | per segment accuracy for non-regular residues |
| BAD | percentage of confused HELIX/STRAND residues (helix predicted as strand, strand predicted as helix) |
| infoO | information index accuracy (percentage of observed) |
| infoP | information index accuracy (percentage of predicted) |
| corrH | Matthews correlation index for helix |
| corrE | Matthews correlation index for strand |
| corrL | Matthews correlation index for loop |
| var | variance over all proteins (1/N-1)*( score(i) - |
| sig | sigma (standard deviation) over all proteins (sqrt[var]) |
| errsig | significant differences ( standard dev / sqrt(Nprot) ) |