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Gene finding
Gene finding with similarity
Gene finding in Bacteria
Gene finding in Viruses
Next Generation
Gene search
Gene explorer
Protein location
RNA structure
Protein structure
Multiple alignment
Analysis of expression data
Plant promoter database
Search and map repeats
Extracting known SNPs



Bacterial Promoter, Operon and Gene Finding

Solovyev V, Salamov A. (2011) Automatic Annotation of Microbial Genomes and Metagenomic Sequences. In Metagenomics and its Applications in Agriculture, Biomedicine and Environmental Studies (Ed. R.W. Li), Nova Science Publishers, p.61-78.

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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