BASys: Bacterial Annotation System

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Welcome to BASys!
BASys (Bacterial Annotation System) is a web server that performs automated, in-depth annotation of bacterial genomic (chromosomal and plasmid) sequences. It accepts raw DNA sequence data and an optional list of gene identification information and provides extensive textual and hyperlinked image output. BASys uses more than 30 programs to determine nearly 60 annotation subfields for each gene, including gene/protein name, GO function, COG function, possible paralogues and orthologues, molecular weight, isoelectric point, operon structure, subcellular localization, signal peptides, transmembrane regions, secondary structure, 3-D structure, reactions, and pathways. The textual annotations and images that are provided by BASys can be generated in approximately 24 hours for an average bacterial chromosome (5 Megabases).
Some sample chromosome maps and annotations created by BASys are available in the Examples.

Please cite: Van Domselaar GH, Stothard P, Shrivastava S, Cruz JA, Guo A, Dong X, Lu P, Szafron D, Greiner R, Wishart DS.BASys: a web server for automated bacterial genome annotation. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W455-9.

Note: BASys is currently experiencing a heavy submission rate and queue times can be up to several weeks, so please be patient. We are in the process of migrating BASys to faster servers to keep pace with the increased submission rate. The annotation results more than 2 months old will be deleted from the server. Thank-you for your patience and understanding, and thanks for using BASys!

BASys Queue Information:- Currently 21 submissions are in queue.

BASys Chromosome Submission

For assistance on running BASys you may wish to check out the BASys HOWTO.

Email Address (Required)

An email address is required to notify you of progress and results.

*Email Address:

Taxonomy (Fields marked with * are required)


*Chromosome Identifier:	(for identifying output files)

*Gram Stain:	Positive Negative

Genus:

Species:

Strain:

Description:

Chromosome (Required)

Upload your FASTA-formatted bacterial chromosome sequence (Example) :

Chromosome is:	Circular Linear
Genetic Code:

Gene Identification (Optional)

BASys can predict protein coding regions from the chromosome sequence using Glimmer (default),
or
choose one of the following:

FASTA Nucleotide Coding Regions File

You can supply BASys with a FASTA-formatted Nucleotide Coding Regions File using the NCBI ".ffn" format. BASys requires the definition line be in the format ">identifier:cstart-end name "
where:

identifier (optional) a unique gene identifier,
c specifies that the coding sequence is on the complementary strand,
start specifies the start location on the direct strand of the chromosome
end specifies the end location on the direct strand of the chromosome, and
name (optional) specifies the gene name.

Upload your FASTA nucleotide coding regions file (Example)

Generate BASys GENECARD accessions	Automatically From this file
Use nucleotide coding sequence data	From ChromosomeFrom this file

BASys Gene Identification Table


You can supply BASys with a TAB-delimited Gene Identification Table like so: START END STRAND IDENTIFIER name 332 805 + 11496586 mob 4373 4257 - 11496606
Upload your BASys Gene Identification Table (Example)

GeneMark HMM Gene Identification Table


If you are submitting phage genomes, you can supply BASys with the gene predictions obtained from the GeneMark HMM website. GeneMark HMM predictions look like this: Predicted genes Gene Strand LeftEnd RightEnd Gene Class # Length 1 - 1 2115 2115 1 2 + 2128 2394 267 1 3 - 2378 2656 279 1 4 + 3225 3440 216 1 5 + 3528 3779 252 1 6 - 3879 5702 1824 1 7 - 5840 6220 381 1
Upload your GeneMark HMM Gene Identification Table (Example)

Questions and comments are welcome. Please contact:
Canadian Bioinformatics Help Desk: info [at] gchelpdesk.ualberta.ca
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