334
V. Mittard-Runte et al.
Table 9.3
Existing bacterial gene finding software. The implemented strategy is depicted as I (intrinsic) and S (similarity based), the availability as D (available
for download) or O (accessible online via web-interface)
Gene finding programs
Program
I
S
Comments
A
URL (in 12.2008)
Critica (Badger and Olsen 1999)
+
+
Identifies genes based on
synonymous substitution rate
D
http://www.ttaxus.com/software.html
EasyGene (Larsen and Krogh 2003)
+
+
Employs HMMs, training set
derived by BLAST search
O
http://www.cbs.dtu.dk/services/EasyGene/
GeneMark.hmm/S (Lukashin and
Borodovsky 1998, Delcher et al. 1999)
+
–
Uses HMMs
O
http://exon.gatech.edu/GeneMark/
Gismo (Krause et al. 2007)
+
+
Combines Pfam search with SVM D
http://www.cebitec.unibielefeld.de/brf/gismo/gismo.html
Glimmer-3 (Delcher et al. 1999)
+
–
Employs interpolated context
model. Uses dynamic programming to reduce overlapping
genes and to refine gene starts
D
http://www.cbcb.umd.edu/software/glimmer/
MetaGene (Noguchi et al. 2006)
+
Employs pre-trained, GC content
dependent codon-usage model.
Applicable also for metagenomic fragments and draft
genomes
D+O
http://metagene.cb.k.u-tokyo.ac.jp
Rast (Aziz et al. 2008)
+
+
Combines Glimmer-2 with
homology searches
O
http://rast.nmpdr.org/
Reganor (McHardy et al. 2004b)
+
+
Combines Glimmer-2 and Critica
O
https://www.cebitec.unibielefeld.de/groups/brf/software/reganor/
RescueNet (Suzek et al. 2001)
+
+
Uses SOM
D
http://bioinf.nuigalway.ie/RescueNet/
SearchForRNAs (Niels Larsen et al.,
unpublished)
Identifies rRNA genes
Available from author upon request.
tRNAscan-SE (Lowe and Eddy 1997)
Predicts tRNA genes using
covariance models
D+O
http://lowelab.ucsc.edu/tRNAscan-SE/
ZCurve (Guo et al. 2003)
+
–
Employs LDA. Performs
Z-transformation of DNA
D
http://tubic.tju.edu.cn/Zcurve_B/
SVM: Support Vector Machine; SOM: Self-Organizing Map
V. Mittard-Runte et al.
Table 9.3
Existing bacterial gene finding software. The implemented strategy is depicted as I (intrinsic) and S (similarity based), the availability as D (available
for download) or O (accessible online via web-interface)
Gene finding programs
Program
I
S
Comments
A
URL (in 12.2008)
Critica (Badger and Olsen 1999)
+
+
Identifies genes based on
synonymous substitution rate
D
http://www.ttaxus.com/software.html
EasyGene (Larsen and Krogh 2003)
+
+
Employs HMMs, training set
derived by BLAST search
O
http://www.cbs.dtu.dk/services/EasyGene/
GeneMark.hmm/S (Lukashin and
Borodovsky 1998, Delcher et al. 1999)
+
–
Uses HMMs
O
http://exon.gatech.edu/GeneMark/
Gismo (Krause et al. 2007)
+
+
Combines Pfam search with SVM D
http://www.cebitec.unibielefeld.de/brf/gismo/gismo.html
Glimmer-3 (Delcher et al. 1999)
+
–
Employs interpolated context
model. Uses dynamic programming to reduce overlapping
genes and to refine gene starts
D
http://www.cbcb.umd.edu/software/glimmer/
MetaGene (Noguchi et al. 2006)
+
Employs pre-trained, GC content
dependent codon-usage model.
Applicable also for metagenomic fragments and draft
genomes
D+O
http://metagene.cb.k.u-tokyo.ac.jp
Rast (Aziz et al. 2008)
+
+
Combines Glimmer-2 with
homology searches
O
http://rast.nmpdr.org/
Reganor (McHardy et al. 2004b)
+
+
Combines Glimmer-2 and Critica
O
https://www.cebitec.unibielefeld.de/groups/brf/software/reganor/
RescueNet (Suzek et al. 2001)
+
+
Uses SOM
D
http://bioinf.nuigalway.ie/RescueNet/
SearchForRNAs (Niels Larsen et al.,
unpublished)
Identifies rRNA genes
Available from author upon request.
tRNAscan-SE (Lowe and Eddy 1997)
Predicts tRNA genes using
covariance models
D+O
http://lowelab.ucsc.edu/tRNAscan-SE/
ZCurve (Guo et al. 2003)
+
–
Employs LDA. Performs
Z-transformation of DNA
D
http://tubic.tju.edu.cn/Zcurve_B/
SVM: Support Vector Machine; SOM: Self-Organizing Map