The ERPIN server: an interface to profile-based RNA motif identification
Lambert, A., Fontaine, J., Legendre, M., Leclerc, F., Permal, E., Major, F., Putzer, H., Delfour, O., Michot, B., Gautheret, D. (2004) Nucleic Acids Research.
ABSTRACT
ERPIN is an RNA motif identification program that takes an RNA sequence alignment as an input and identifies related sequences using a profile-based dynamic programming algorithm. ERPIN differs from other RNA motif search programs in its ability to capture subtle biases in the training set and produce highly specific and sensitive searches, while keeping CPU requirements at a practical level. In its latest version, ERPIN also computes E-values, which tell biologists how likely they are to encounter a specific sequence match by chance—a useful indication of biological significance. We present here the ERPIN online search interface ( http://tagc.univ-mrs.fr/erpin/ http://tagc.univ-mrs.fr/erpin/). This web... Show Full AbstractFigures From Article (2)
FIGURE CAPTION
Figure 2. Screen shot of an ERPIN output page for a type II tRNA motif search. (A) sequence name in FASTA search database; (B) strand direction of hit; (C) position of hit; (D) score of hit; (E) E-value of hit; (F)... Show Full Caption 
FIGURE CAPTION
Figure 1. Screen shot of the ERPIN server input form. The ‘polyadenylation site’ motif was selected and information related to this motif is displayed. (A) available motifs; (B) target database selection; (C) motif-related information; (D) selection of search strand. Tables From Article (1)
TABLE CAPTION
Table 1.. Search performance of available RNA motifs | RNA motif | Time (s/Mb)a | FPs/100 Mbb | Sensitivity (%)c |
|---|---|---|---|
| tRNA, generic nuclear | 7.88 | 9.81e − 04 | 97.84 (1086/1110) |
| tRNA, type I | 3.71 | 1.04e − 01 | 98.34 (887/902) |
| tRNA, type II | 1.38 | 6.09e − 07 | 94.69 (196/207) |
| 5S rRNA, bacterial | 4.98 | 1.21e − 10 | 92.59 (275/297) |
| 5S rRNA, eukaryotic | 4.98 | 1.46e − 29 | 88.92 (281/316) |
| 5S rRNA, archaeal | 4.23 | 8.61e − 14 | 96.30 (52/54) |
| 23S rRNA, sarcin-ricin loop | 3.76 | 1.74e − 01 | 86.15 (56/65) |
| SRP RNA domain IV | 1.45 | 2.10e − 01 | 95.93 (165/172) |
| SECIS | 22.91 | 6.38e + 01 | 82.79 (101/122) |
| IRE, uptake form | 1.98 | 1.13e − 03 | 95.00 (19/20) |
| IRE, storage form | 2.93 | 2.25e − 07 | 84.62 (11/13) |
| Polyadenylation site | 0.44 | 4.62e + 02 | 63.52 (1478/2327) |
| T-box | 26.58 | 1.14e + 01 | 92.14 (129/140) |
| snoRNA, C/D box archaeal | 29.22 | 1.70e − 01 | 76.39 (165/216) |
| snoRNA, C/D box human–mouse | 12.54 | 7.98e + 01 | 77.67 (80/103) |
| snoRNA, C/D box yeast | 11.16 | 7.75e + 02 | 60.71 (17/28) |
| Rho-independent terminator | 28.11 | 4.05e + 02 | 86.26 (1036/1201) |
| Hammerhead 1 | 28.13 | 1.90e + 01 | 100.00 (1657/1657) |
| Hammerhead 3 | 6.37 | 4.32e + 02 | 99.83 (2346/2350) |
| miRNA, let7 family | 19.40 | 1.48e − 02 | 86.67 (26/30) |
| miRNA, lin4 family | 5.81 | 9.84e − 02 | 81.82 (18/22) |
| miRNA, mir1 family | 3.35 | 4.92e − 05 | 72.73 (8/11) |
| miRNA, mir9 family | 26.23 | 1.22e − 01 | 72.73 (8/11) |
| miRNA, mir15-16-195 family | 4.94 | 2.17e − 08 | 77.78 (7/9) |
| miRNA, mir30 family | 3.58 | 5.24e − 03 | 93.33 (14/15) |
| miRNA, mir106 family | 4.32 | 3.24e − 06 | 80.00 (8/10) |
| miRNA, mir182-183-228-263 family | 4.05 | 1.53e − 02 | 75.00 (6/8) |
| miRNA, mir166 family, plants | 31.47 | 6.26e − 02 | 85.71 (12/14) |
| miRNA, mir160 family, plants | 6.72 | 8.99e − 07 | 62.50 (5/8) |
| miRNA, mir156 family, plants | 12.64 | 7.66e − 09 | 71.43 (10/14) |
| CRE, poliovirus | 4.06 | 9.03e − 28 | 100.00 (5/5) |
| IRES, poliovirus | 3.09 | 1.02e − 194 | 100.00 (3/3) |
| TAR, HIV-1 | 2.33 | 2.60e − 09 | 100.00 (24/24) |
| PSTVd RNA, substructure | 18.74 | 2.09e − 200 | 100.00 (89/89) |
