. 2009 May 21;37(Web Server issue):W193–W201. doi: 10.1093/nar/gkp388

Table 1.

Performance comparison of MoPP with five popular motif finders on mycobacterial datasets

Regulon	Consensus	Size	MoPP^a	YMF	PRISM	SCOPE	Oligo	MEME
`MycoSigA-10`	`TATAMT`	`95`	`TAYAVT (1)^b`	`TATtrW (5) TATtAW (6)`	`tTAcAAT (3)`	`TANDVTgk (2)`	`TAgACT (1) TAcAAT (2)`	`TAgACT (1)`
`MycoSigA-35`	`TTGACW`	`95`	`cTKGAC (1) cTBGAC (3)`	`TTGACW (6)`	`gnhWTGACW (1)`	`wyTTGMMW (1)`	`TTGACT (2)`	`TTGACT (1)`
`MycoSigA50bp`	`TATAMT`	`95`	`TATACT (2) TAKACT (3)`	`TAgWCW (14)`	`tTAcAAT (14)`	`ataTHDMAY (2)^c`	`TAgACT (6)`	`TATtAT (11)`
	`TTGACW`		`TRACTa (1) TaKACT (3)`	`TaGWCW (14) TWGACW (22)`			`TTGACT (4)`	`TTGACT (2)`
`MycoSigD-10`	`WNATGT^d`	`6`	`gTTATG (1) gTTABG (4)`	`ACATaT (15)`
`MycoSigD-35`	`GTAACG`	`6`	`gGWAWC (3)`	`gGTAAC (2)`			`GTAACG (1)`	`GTAACG (1)`
`MycoSigH-10`	`SGTTS`	`10`	`tCGTT (1) gCGKT (2)`	`SGTTar (21)`	`cGGTT (3)`	`cGGTT (3)`	`gCGTT (1)`	`cCGTT (2)`
`MycoSigH-35`	`SGGAAC`	`10`	`GGGAAt (1) GGGAAY (2)`	`GGGAAC (1) GGGAAY (2)`	`CGGAA (2)`	`CGGAA (2)`	`GGGAAC (1)`	`GGGAAC (1)`
`MycoSigL-10`	`CGTGTC`	`5`	`CGTGTC (1)`	`GTGTCa (5)`			`GTGTCa (1) CGTGTC (2)`	`GTGTCa (1)`
`MycoSigL-35`	`TGAACC`	`5`	`tTGAAC (1) bTGAAC (2)`	`TGWACY (3) TGAACY (5)`	`TGAAC (1)`	`bTGAAC (1)`	`TGAACC (1)`	`cTGAAC (1)`
`mS_r`			`1.0`	`0.4`	`0.5`	`0.5`	`0.8`	`0.8`

^aWeeder could not be compared since the background file was not available.

^bPattern is highlighted in bold if it matches the consensus with not more than one mismatch and ranks among top five. Number in parenthesis indicates rank of the pattern.

^cNot considered a match since ≥80% of the matching residues are degenerate nucleotides or matching with degenerate nucleotides.

^dAccording to MtbRegList (www.usherbrooke.ca/vers/MtbRegList).