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The programs usage in Scientific publications
fgenesB
- Pattern/Markov chain-based bacterial operon and gene
prediction [Help]
[Example]
BPROM - Prediction of bacterial promoters
[Help]
[Example]
AbSplit
- Separating archea and bacterial genomic sequences
[Help]
[Example]
FindTerm
- Finding Terminators in bacterial genomes
[Help]
[Example]
Visualization of FgenesB annotation using CGView
[Example]
Bacterial GenomeSequence Explorer - Visualization of Bacterial genomes information
[Help]
All bacteria genomes annotations
General scheme of bacterial genome annotation
-(automatic pipeline - Fgenesb_annotator)
Human Microbiome gene prediction
Softberry Microbiome Annotation Database
FGENESB is the fastest (E.coli genome
is annotated in ~14 sec) and most accurate ab initio bacterial
operon and gene prediction program available - for more details, see
FGENESB
help. It uses genome-specific parameters learned by
FGENESB-train
script, which requires only DNA sequence from genome of interest
as an input. It automatically creates a file with gene prediction
parameters for analyzed genome. It took only a few minutes to
create such file for E.coli genome using its sequence. If you
need parameters for your new bacteria, please contact Softberry -
we can include them in the web list.
In current FGENESB version, complex operon prediction
model is realized based on gene distances. It can recognize accurately
70% of single transcription units and define exactly about 50% of
operons (~92% partially). Increasing accuracy of operon identification is done
by using prediction of promoter and terminator and analyzing neighbor location of genes in many bacterial genomes.
We developed new FGENESB-Annotator script that
finds similar proteins in public databases and annotates predicted
genes. This script can also identify low scoring genes if they have
known homologous protein. The script annotates CDS, Promoters,
Terminators, Operons,
tRNA and RRNA. For more details, see FgenesB-Annotator manual.
The annotation can be produced in GenBank
format
(see example later) and exported to
different Bacterial Genome Browsers such as Artemis (Sanger Center) or
Softberry GenomeSequence Explorer
FGENESB-Annotator script includes possibility to
atomatically annotate sets of sequences
generated by sequencing some Bacterial Community scaffolds. To separate
archebacterial sequences from bacterial sequences
that required different gene finding parameters use
ABSplit program.
Together, FGENESB gene finding program and Train and
Annotator scripts costitute FGENESB pipeline - the most comprehensive
tool for prokaryotic genome annotation. Description of the pipeline
is given here.
EXAMPLE:
Annotation of Bacillus
anthracis A2012 main chromosome by FgenesB-Annotator
script.
......... Annotation
in GenBank format
Examples of annotation
of operons and genes for other bacteria
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