TABLE 2.
Usage characteristics of the tools analyzed here
| Tool | Multifasta | Big files | Shows promoter core | Score or probability | Uppercase only | Output format | Execution time | Follow up | Interface | Comment(s) |
|---|---|---|---|---|---|---|---|---|---|---|
| BPROM | No | Yes | Yes | Yes | No | Text on screen | Fast | Progress on screen | Webform, simple, intuitive | Multifasta not supported and sequence boxes are not shown; difficult to process the results |
| bTSSfinder | Yes | Yes | Yes | Yes | No | Text file, GFF file, BED file | Fast | Progress on screen | Login needed, webform, simple, intuitive | Flexible configurations of cutoff values; results saved for 1 week; Linux tool available for download; it needs a large promoter sequence (−200, +50, related to the putative TSS) |
| BacPP | Yes | No | No | Yes | No | Text on screen or text file | Fast | N | Login needed, webform, simple, intuitive | Short tests per time |
| Virtual Footprint | No | Yes | Yes | Yes | No | Text on screen | Medium fast | Progress on screen | Webform, many fields, and option in the screen | Integrated with a large PWM database of TFBS; applicable to many species; limited to the position weight matrix available |
| IBBP | No | Yes | It shows the putative TSS | Yes | No | Text file | Fast | Progress on screen | Command line | Windows SO only execution; requires the manual input files; training and test procedures are separated; fast for big files; it can be used as an approach to the initial prediction of any type of promoters |
| iPro70-FMWin | Yes | Yes | No | Yes | No | Text on screen | Fast | No | Webform, simple, intuitive | High accuracy |
| 70ProPred | Yes | Yes | No | No | Yes | Text on screen | Fast | No | Webform, simple, intuitive | High accuracy; it does not accept a file as input, just text on a form |
| CNNProm | Yes | Yes | No | Yes | Yes | Text on screen | Long time (for genomes), fast for multifasta | No | Webform, simple, intuitive | Useful for large sequences (genomes); without a follow-up display; multifasta not supported and sequence boxes are not shown; difficult to process the results |
| MULTiPly | Yes | Yes | No | No | No | Text on screen or text file | Medium time | Progress on screen, job ID to find the result later | Webform, simple, intuitive | Good accuracy; it saves the result; time-consuming for large sequences |
| iPromoter-2L | Yes | Yes | No | No | No | Text on screen | Fast | Progress on screen | Webform, simple, intuitive | Good accuracy |