Table 2.
Algorithm decisions for Influenza A clinical sample identified previously using a manual method for SubSeq, ProSeq identification Task(I), ProSeq grouping Task(II) and pathogen determination Task(III)
| Sample name | ProSeq | No. of Sub | SubSeq organism identification and Uniqueness, Bit score | Task(I) | Task(II) | Task(III) |
|---|---|---|---|---|---|---|
| A/Colorado /360/05 | HA3 | 1 | H3N2 TA,1031 | H3N2 TA | (NY) SU H3N2 TA | POSITIVE H3N2 |
| NA2 | 1 | A/NewYork/98/04(NY) SU,1570 | (NY) SU | |||
| M | 4 | 2 Flu A TA,69.7 128 | H3N2 TA | |||
| 2 H3N2 TA,125 393 | ||||||
| A/Qatar /2039/05 | HA3 | 1 | A/Qatar/2039/05(QA) SU,1080 | (QA) SU | (QA) SU H3N2 TA | POSITIVE H3N2 |
| NA2 | 2 | 2 H3N2 TA,643 919 | H3N2 TA | |||
| M | 4 | 2 H3N2 TA,505 272 | H3N2 TA | |||
| 2 Flu A TA,115 77.7 | ||||||
| A/Guam /362/05 | HA3 | 1 | A/Guam/362/05(GA) SU,1066 | (GA) SU | (GA) SU H3N2 TA | POSITIVE H3N2 |
| NA2 | 1 | H3N2 TA,1610 | H3N2 TA | |||
| M | 4 | 2 H3N2 TA,240 397 | H3N2 TA | |||
| 2 Flu A TA,79.2 79.2 | ||||||
| A/Italy /384/05 | HA3 | 1 | A/Italy/384/05(IT) SU, 1017 | (IT) SU | (IT) SU (NY) SU H3N2 TA | POSITIVE H3N2 |
| NA2 | 1 | A/NewYork/371/04(NY) SU,1494 | (NY) SU | |||
| M | 3 | 2 H3N2 TA, 461 359 | H3N2 TA | |||
| Flu A TA,74.5 | ||||||
| A/Turkey/2108/05 | HA3 | 1 | A/Turkey/2108/05(TU) SU,952 | (TU) SU | (TU) SU H3N2 TA | POSITIVE H3N2 |
| NA2 | 1 | H3N2 TA,1363 | H3N2 TA | |||
| M | 3 | 2 H3N2 TA,412 239 | H3N2 TA | |||
| Flu A TA,76.1 | ||||||
| A/Korea/298/05 | HA3 | 1 | A/Korea/298/05(KO) SU,1011 | (KO) SU | (KO) SU (NY) SU H3N2 TA | POSITIVE H3N2 |
| NA2 | 3 | A/NewYork/98/04(NY) SU,243 | (N1) SU | |||
| 2 Flu A TA,110 98.3 | ||||||
| M | 4 | 2 Flu A TA,66.6 76.1 | H3N2 TA | |||
| 2 H3N2 TA,328 255 | ||||||
| A/Japan /1383/05 | HA3 | 1 | A/Japan/1383/05(JA) SU,935 | (JA) SU | (JA) SU H3N2 TA | POSITIVE H3N2 |
| NA2 | 1 | H3N2 TA,1369 | H3N2 TA | |||
| M | 5 | 3 Flu A TA,125 114 76.1 | H3N2 TA | |||
| 2 H3N2 TA,175 247 | ||||||
| A/Ecuador /1968/04 | HA3 | 1 | H3N2 TA,1071 | H3N2 TA | H3N2 TA | POSITIVE H3N2 |
| NA2 | 2 | H3N2 TA,1584 109 | H3N2 TA | |||
| M | 4 | 3 Flu A TA,158 164 104 | H3N2 TA | |||
| H3N2 TA,131 | ||||||
| A/Iraq /34/05 | HA3 | 1 | A/Iraq/34/05(IR) SU,1028 | (IR) SU | (IR) SU H3N2 TA | POSITIVE H3N2 |
| NA2 | 3 | 2 H3N2 TA,125 1402 | H3N2 TA | |||
| Flu A TA,109 | ||||||
| M | 5 | 3 H3N2 TA,137 350 234 | H3N2 TA | |||
| 2 Flu A TA,131 74.5 | ||||||
| A/Peru /166/05 | HA3 | 1 | A/Peru/166/05(PU) SU,1061 | (PU) SU | (PU) SU H3N2 TA | POSITIVE H3N2 |
| NA2 | 1 | H3N2 TA,1686 | H3N2 TA | |||
| M | 3 | H3N2 TA,508 | H3N2 TA | |||
| Flu A TA,76.1 | ||||||
| A/NewYork/461/2005 SU,247 |
Note: Within a row the first listing of a specific strain was followed by a two-letter abbreviation used in the remaining columns of that row.