Table 1.
Motifs utilized by ReTe at present. Some of the Motifs are used in the ‘fragment threading’, others in LTR search or in putein construction
| Name | Used in | Characteristics |
|---|---|---|
| AcidMotif | RetroVID | Compares to conserved amino acid sequence |
| AcidNNMotif | RetroVID | Uses neural network trained on known peptides |
| SplitAcidMotif | RetroVID | Like several AcidMotifs at prescribed distances |
| BaseMotif | RetroVID, LTRID | Compares to conserved nucleotide sequence |
| HyPhobMotif | RetroVID | Searches for hydrophobic region in Gag |
| LTRMotif | RetroVID | Encapsulates LTR candidate found by LTRID |
| PPTMotif | RetroVID | Special algorithm for polypurine tract |
| SpliceAcceptorMotif | ORFID | Searches for splice acceptor consensus |
| SpliceDonorMotif | ORFID | Searches for splice donor consensus |
| SlipperyMotif | ORFID | Searches for XXXYYYZ |
| ProteaseCleavageMotif | ORFID | Searches for wPf, fPv and yPi |
| PseudoKnotMotif | ORFID | Searches for pseudoknot-like structures |
| FrameShifterMotif | ORFID | Combination of SlipperyMotif and PseudoKnotMotif |
| PuteinStartMotif | ORFID | Compares to leading amino acid sequences in known proteins |
| PuteinStartMotif | ORFID | Compares to trailing amino acid sequences in known proteins |
| SiSeqMotif | ORFID | Scores with weight matrix for signal sequence of von Heijne |