Table 1.
Feature comparison between GAMOLA2 and three other annotation suites.
| GAMOLA2 | PROKKA | ConsPred | RAST/myRAST | |
|---|---|---|---|---|
| RUNTIME ENVIRONMENT | ||||
| GUI |  |
|
|
|
| Visualization of annotation |
(a)
|
|
 (b)
|
(c)
|
| Local PC | |
|
|
|
| Server-client/terminal | |
|
|
|
| Cloud | |
|
|
|
| Web-based | |
|
|
|
| Multi-threaded | |
|
|
|
| Off-line capability | |
|
|
|
| Re-use previous results | |
|
|
|
| Filter Blast results |
(d)
|
|
(e)
|
|
| GENE MODEL PREDICTION | ||||
| Glimmer 2/3 | |
|
|
|
| Prodigal | |
|
(f)
|
|
| Critica | |
|
|
|
| GeneMark | |
|
|
|
| RAST | |
|
|
|
| Intergenic Blast | |
|
|
|
| Blast Homology based gene prediction | |
|
|
|
| RBS | |
|
|
|
| External gene model |
(g)
|
|
|
|
| Additive prediction | |
|
|
|
| Rule based prediction | |
|
|
|
| FUNCTIONAL ANALYSES | ||||
| Blast/Blast-Plus | |
|
|
|
| Multiple Blast flavors | |
(h)
|
(h)
|
|
| Custom Blast databases | |
|
(i)
|
|
| COG | |
|
|
|
| Multiple COG databases |
(j)
|
|
|
|
| eggnog |
(k)
|
|
|
|
| Pfam (HMMER2/3) | |
|
|
|
| TIGRfam | |
|
|
|
| FIGfam | |
|
|
|
| Selection of multiple databases |
(l)
|
|
|
|
| Gene Ontology descriptor | |
|
|
|
| InterPro descriptor | |
|
|
|
| InterProScan | |
|
|
|
| EC number | |
|
|
|
| KEGG | |
|
|
|
| Metabolic reconstruction | |
|
|
|
| STRUCTURAL ANALYSES | ||||
| tRNA | |
|
|
|
| rRNA | |
|
|
|
| Non-coding RNAs | |
|
|
|
| Transmembrane helices | |
|
|
|
| Signal Peptide Cleavage Sites | |
|
|
|
| Rho-independent terminators | |
|
|
|
| CRISPRs | |
|
|
|
| Vector screen | |
|
|
|
| INPUT FORMATS AND SEQUENCE HANDLING | ||||
| FASTA | |
|
|
|
| msFASTA | |
|
|
|
| Genbank | |
|
|
|
| msGenbank | |
|
|
|
| Concatenate sequences | |
|
|
|
| Create concatenated sequence clusters | |
|
|
|
| Prevent gene model bleeding across contigs | |
|
|
|
| Update Genbank files | |
|
|
|
| OUTPUT | ||||
| Genbank | |
|
(m)
|
|
| GFF tracks | |
|
|
|
| EMBL | |
|
|
|
| All features displayed | |
|
|
|
| Embedded feature descriptors | |
|
|
|
| Feature csv/tsv file |
(n)
|
|
|
|
| Feature Excel file |
(n)
|
|
|
|
| Log and Error files |
(o)
|
|
|
|
| Statistic file |
(n)
|
|
|
|
| OTHER FEATURES | ||||
| Create custom Blast databases | |
|
|
|
| Rotate Genbank files | |
|
|
|
| Prepare for Sequin submission | |
|
|
|
| Annotation transfer | |
|
|
|
| Functional Metagenome analysis | |
|
|
|
(a)
Via enhanced Artemis genome viewer;
(b)
static HTML sites to KEGG and KO;
(c)
custom browser;
(d)
custom filter;
(e)
automatic;
(f)
default;
(g)
internal and GFF format;
(h)
blastp only;
(i)
NCBI nr only;
(j)
COG2003, COG2008, COG2014, arCOG, arCOG2014, POG2013;
(k)
planned in next release;
(l)
for Pfam and TIGRfam;
(m)
partial feature only;
(n)
available as separate software, integration in the next release update;
(o)
Gamola2 creates verbose error logs.