BG7 usage for bacterial genome annotation

Question

[mark.rose]

Hi All

Is anyone regularly using BG7 for bacterial genome annotation? I'm not seeing many posts on it and, having downloaded it and tried to run it on the included test data, ran into several execution script errors which I think would have been fixed if it were being widely used. It's strategy is interesting but I don't know how deep a hole I'm willing to go down to debug it.

Thanks
Mark

[natasha.sernova]

See these papers about BG7:

Gene calling and bacterial genome annotation with BG7

http://ohnosequences.com/publications/bg7-chapter-bacterial-pangenomics.pdf - from 2014

BG7: A New Approach for Bacterial Genome Annotation Designed for Next Generation Sequencing Data

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0049239 - from 2012

[mark.rose]

Yes, I've seen these papers. The first one is more practical in that it purports to describe how to execute BG7. That's where I run into trouble. In what I have downloaded from github, there is no executable called "BG7", only "bg7", which is a shell script and does take any of the commands (create, publish, run) indicated in the paper. There is also a "BG7.jar" file, which, likewise, does not appear to accept any of these commands, Is there something I must do to prepare the BG7 directory prior to use to create the BG7 application. So far the papers instructions have not been helpful. Here is a tree of the BG7 directory I have downloaded.

$ tree -CAt BG7/
BG7/
├── bg7_example_input_files.zip
├── bin
│   ├── bg7
│   └── installers
│       └── amzn-linux
│           └── bg7-installer
├── build.xml
├── executionsTemplate.xml
├── GenBankExternalData.xml
├── genetic_code.txt
├── jars
│   └── BG7.jar
├── lib
│   ├── Bio4jModel-1.0-jar-with-dependencies.jar
│   ├── BioinfoUtil-1.0-jar-with-dependencies.jar
│   ├── BioinfoXML-1.0-jar-with-dependencies.jar
│   ├── commons-codec-1.4.jar
│   ├── commons-httpclient-3.1.jar
│   ├── commons-logging-1.1.1.jar
│   ├── CopyLibs
│   │   └── org-netbeans-modules-java-j2seproject-copylibstask.jar
│   ├── Era7BioinfoXML-1.0-jar-with-dependencies.jar
│   └── nblibraries.properties
├── README.md
└── src
    └── com
        └── era7
            └── bioinfo
                └── annotation
                    ├── embl
                    │   └── ExportEmblFiles.java
                    ├── gb
                    │   ├── Control5ColumnsGenBankFilesQuality.java
                    │   ├── ControlGenBankFilesQuality.java
                    │   ├── Export5ColumnsGenBankFiles.java
                    │   ├── ExportGenBankFiles.java
                    │   ├── GBCommon.java
                    │   └── ImportGenBankFiles.java
                    ├── RemoveDismissedGenes.java
                    ├── RemoveDuplicatedGenes.java
                    ├── SolveOverlappings.java
                    ├── AutomaticQualityControl.java
                    ├── BasicQualityControl.java
                    ├── BG7.java
                    ├── FillDataFromUniprot.java
                    ├── FixFastaHeaders.java
                    ├── FixFastaHeadersQC.java
                    ├── GeneEValuePair.java
                    ├── GenerateCSVFile.java
                    ├── GenerateFastaFiles.java
                    ├── GenerateGffFile.java
                    ├── GetIntergenicSequences.java
                    ├── GffLine.java
                    └── PredictGenes.java