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Protocols

FGENESB specifications

Information


Unique identifier OMICS_29535
Name FGENESB
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data A nucleotide sequence.
Input format FASTA
Output data A list of the locations of predicted protein coding, rRNAs, tRNAs genes, operons, promoters and terminators.
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Additional information


http://www.softberry.com/berry.phtml?topic=fgenesb&group=help&subgroup=gfindb

FGENESB citations

 (111)
library_books

Identification of two different chemosensory pathways in representatives of the genus Halomonas

2018
BMC Genomics
PMCID: 5907407
PMID: 29669514
DOI: 10.1186/s12864-018-4655-4

[…] iology, https://toolkit.tuebingen.mpg.de/tprpred) [].Operon prediction was based on directions of adjacent genes, distribution of intergenic distances and presence of predicted promoter regions using FGENESB (Softberry) []. […]

library_books

The crystal structure of XdpB, the bacterial old yellow enzyme, in an FMN free form

2018
PLoS One
PMCID: 5891007
PMID: 29630677
DOI: 10.1371/journal.pone.0195299

[…] nalyzed using LigPlot+ [] with the symmetry-related pentapeptide as a ligand. GenBank was searched by the blastp and DELTA blast tool []. Bacterial Operon and Gene Prediction was done by the Software FGENESB []. Operator-like sequence characteristics for the TetR family proteins were determined based on the results obtained by Deng at al. [] and promoters were analyzed by the MacLellan's method [] […]

library_books

Characterization of the pgf operon involved in the posttranslational modification of Streptococcus mutans surface proteins

2018
Sci Rep
PMCID: 5856776
PMID: 29549320
DOI: 10.1038/s41598-018-23170-3

[…] ative promoters driving transcription of pgfS, pgfM1, pgfE and pgfM2, and ARNold software (http://rna.igmors.u-psud.fr/toolbox/arnold/) was used to determine putative transcriptional terminators. The FGENESB bacterial operon and gene prediction software (http://www.softberry.com/berry.phtml?topic = fgenesb&group = programs&subgroup = gfindb) was used to predict the co-transcription of pgfS, pgfM1, […]

library_books

Diversity of Gene Clusters for Polyketide and Nonribosomal Peptide Biosynthesis Revealed by Metagenomic Analysis of the Yellow Sea Sediment

2018
Front Microbiol
PMCID: 5835077
PMID: 29535686
DOI: 10.3389/fmicb.2018.00295

[…] e sequences as described above and used for phylogenetic tree construction (allow 4 mismatches in each primer). The taxonomy of 12 contigs was determined with PhyloPythiaS analysis and annotated with fgenesb and BlastX (Patil et al., ). All the contigs were submitted to antiSMASH for further PKS and NRPS gene cluster annotation (Weber et al., ). The 12 contigs were deposited in Genbank and the acc […]

library_books

A bifunctional cellulase–xylanase of a new Chryseobacterium strain isolated from the dung of a straw‐fed cattle

2017
PMCID: 5812240
PMID: 29205864
DOI: 10.1111/1751-7915.13034

[…] Putative genes and operons in the 4643 bp fragment were predicted using FGENESB (Solovyev and Salamov, ). Putative promoter was predicted using BPROM (Solovyev and Salamov, ). Putative signal peptide was detected using SignalP (Petersen et al., ). […]

library_books

Heat Resistance Mediated by pLM58 Plasmid Borne ClpL in Listeria monocytogenes

2017
PMCID: 5663981
PMID: 29104933
DOI: 10.1128/mSphere.00364-17

[…] d using RAST 2.0 (), and genome comparison was performed in SEED Viewer 2.0 (). Prophage prediction was performed using PHASTER (, ), and sequence-based operon prediction of pLM58 was performed using FGENESB (). Visual comparison of AL4E and AT3E chromosomes was generated using BRIG (BLAST ring image generator) (), and pLM58 was visualized using SnapGene Viewer 3.3.4 (GSL Biotech LLC, Chicago, IL) […]

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