BAGET HELP
Introduction

BAGET is a web service designed to facilitate extraction, by molecular geneticists and phylogeneticists, of specific gene and protein sequences from completely determined prokaryotic genomes. Upon selection of a particular prokaryotic organism and gene, two levels of visual gene context information are provided on a single dynamic page: i) a graphical representation of a user defined portion of the chromosome centered on the gene of interest and ii) the DNA sequence of the query gene, of the immediate neighboring genes and the intergenic regions each identified by a consistent color code. The aminoacid sequence is provided for protein-coding query genes. Query results can be exported as a rich text format (RTF) word processor file for printing, archival or further analysis.
BAGET Manual

Step 1. Organism/chromosome selection

BAGET allows to select the genome of every completely sequenced archaea and bacteria available at the NCBI repository. Genomes are selected by chosing the organism species name. When an organim harbors multiple chromosomes, these are appended with the suffix C1, C2, etc. C1 being the largest.

Step 2. Chromosomal sequence interval

BAGET can display a genomic map or user selected size: 2, 5, 10, 15, 20 and 25kb. The default size is 10kb.

Step 3. Gene selection

BAGET offers two modes to select the gene of interest:

A. Search by gene name
The gene of interest can be selected by searching the database with the gene name or a substring of the name. The search is case insensitive. Each gene in the search list can be clicked to generate a report.

B. Gene list
The genes of some genomes are not fully annotated: they are only identified by alphanumeric strings. The gene list browser allows to search genomes sequentially by groups of hundred genes. Each gene in the gene list can be clicked to generate a report.

Step 4. Report generation

A click in the search list or the browser gene list generates a report composed of several elements.

A. Genomic context panel
The genomic context panel consists of a genomic map of user selected length (Step 2). The genes are color coded; the gene of interest in shown in red, the genes in the same orientation as the gene of interest are shown in blue and the genes in the opposite orientation are shown in green. The function of the genes composing the genomic context map can be accessed by mouse hovering.

B. DNA sequence panel
The sequence panel displays the actual DNA sequence of the gene of interest together with the sequence of the immediate upstream and downstream neighbouring genes. The coding sequence color codes are consistent with the genomic context panel. The intergenic sequences are shown in back. Overlapping coding sequences are easily identified by BAGET: the background color of the sequence of the gene of interest indicates the presence and the extent of the overlap.

C. Protein sequence
When the gene of interest encodes a protein, its amino acid sequence is shown in the protein sequence panel.

D. NCBI Link
BAGET generates, for the gene of interest, an external link to the NCBI web repository.

E. Report in RTF format
The whole BAGET report can be exported as a rich text format (RTF) document which can be stored locally and opened with any word processing program.
BAGET Database Update

To ensure maximum freshness, the genomic database used by BAGET is updated daily at 6:00am GMT. The update is fully automated.