Table 1.
Comparison of databases of poly(A) sites
| PolyASite 2.0 | PolyA_DB 3 | APASdb | APADB | PolyASite | |
|---|---|---|---|---|---|
| Content | |||||
| Organisms | H. sapiens | H. sapiens | H. sapiens | H. sapiens | H. sapiens |
| M. musculus | M. musculus | M. musculus | M. musculus | M. musculus | |
| C. elegans | G. gallus | D. rerio | G. gallus | ||
| R. norvegicus | B. belcheri | ||||
| Genome version | hg38 | hg19 | hg19 | hg19 | hg19 |
| mm10 | mm9 | mm9 | mm10 | mm10 | |
| ce11 | galgal4 | Zv_9 | galgal4 | ||
| Rnor_5.0 | v7h2 | ||||
| Number of samples | 221 | 107 | 33 | 8 | 78 |
| 178 | 246 | 8 | 3 | 110 | |
| 22 | 11 | 8 | 1 | ||
| 9 | 2 | ||||
| Number of protocols | 12 | 1 | 1 | 1 | 9 |
| Number of poly(A) clusters | 569 005 | 290 168 | NA | NA | 392 912 |
| 301 001 | 384 337 | 183 225 | |||
| 20 931 | 61 905 | ||||
| 65 909 | |||||
| Functionality | |||||
| Gene search | yes | yes | yes | yes | no |
| Genomic region search | yes | no | no | no | no |
| Genome browser | UCSC | UCSC | GBrowse | JBrowse | - |
| Atlas (sample integration) | yes | yes | no | no | yes |
| Individual samples | yes | no | yes | yes | yes |
| Web | |||||
| Url | https://polyasite.unibas.ch/ | http://exon.umdnj.edu/polya_db/v3/ | http://genome.bucm.edu.cn/utr/ | http://tools.genxpro.net/apadb/ | http://polyasite-v1.scicore.unibas.ch |
| https | yes | no | no | no | no |
| Responsive design | yes | no | no | no | no |
| Latest release | September 2019 | August 2018 | September 2014 | June 2014 | October 2015 |