Table 1 Homology reduction methods and numbers of sequences used by available software. Abbreviations: HR - homology reduction, HP - homology partitioning, TM - thylakoid membrane, TL - thylakoid lumen, IM - inner membrane, OM - outer membrane. *Authors report that the threshold was set to 25% but they use data from MultiP-Schlo created with 40% cutoff.
From: Prediction of protein subplastid localization and origin with PlastoGram
Software | Year | Homology reduction strategy (cutoff) | Final number of sequences | Envelope | Stroma | TM | TL | Plastoglobule |
|---|---|---|---|---|---|---|---|---|
SubChlo | 2009 | CD-HIT HR (60%) | 262 | 40 | 49 | 129 | 44 | - |
ChloroRF | 2010 | CD-HIT HR (60%) | 261 | 40 | 49 | 128 | 44 | - |
SubIdent | 2011 | CD-HIT HR (60%) | 262 | 40 | 49 | 129 | 44 | - |
BS-KNN | 2012 | CD-HIT HR (60%) | 253 | 40 | 46 | 127 | 40 | - |
ChloPred | 2013 | PISCES HR (25%) | 259 | 77 | 60 | 103 | 19 | - |
SCLAP | 2013 | PISCES HR (60%) | 341 | 118 | 72 | 111 | 41 | - |
WS-LCHI | 2014 | CD-HIT HR (60%) | 262 | 40 | 49 | 129 | 44 | - |
MultiP-Schlo | 2015 | CD-HIT HR (40%) | 578 | 199 | 105 | 233 | 34 | 30 |
LNP-Chlo | 2016 | CD-HIT HR (40%*) | 578 | 199 | 105 | 233 | 34 | 30 |
SChloro | 2016 | HP with PSI-BLAST | 367 | 71 (47 IM, 24 OM) | 119 | 131 | 37 | 32 |
EnTrans-Chlo | 2017 | CD-HIT HR (40%*) | 578 | 199 | 105 | 233 | 34 | 30 |
Bankapur &Patil | 2022 | CD-HIT HR (40%) | 578 | 199 | 105 | 233 | 34 | 30 |
