xBASE bacterial genome annotation service

Introduction

This page offers a quick and easy annotation service for bacterial genome sequences. It is particularly suitable for unfinished genome sequences where a similar reference sequence is available. One main advantage this service has over others is speed; an E. coli size sequence should be ready in as little as 20 minutes.

To use, submit a file containing one or more FASTA-formatted nucleotide sequences (contigs produced by a whole genome assembler, for example). To guide gene prediction and annotation, select the closest complete reference sequence for your genome. A link to the finished annotation will be sent to the e-mail address you enter, so please double-check it is correct.

Reference Genome:
Your e-mail address:
FASTA nucleotide sequence(s):
Species name:
Strain identifier:

Gene min length:
Gene max overlap:
Blast evalue cutoff:
Training model:

Methods

The software performs the following steps:

Gene prediction will be performed using Glimmer¹.
tRNA genes will be searched for with tRNAScan-SE².
Ribosomal RNA genes will be searched for with RNAmmer³.
Protein BLAST⁴ is run using the translated coding sequences as a query against the reference sequence you have selected.
The best result for each BLAST search is imported as the gene annotation (if under the user-supplied E-value cutoff).
The resulting file is a GenBank file suitable for loading into a sequence viewer such as Artemis
The sequences are ordered and reverse complemented according to the longest matches against the reference sequence.
A comparison file with concatenated reference and sequence files are produced, suitable for loading into ACT is also produced using MUMMER⁶.

References

If you use this interface for published work, please cite the following references.

Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. 2007 Mar 15;23(6):673-9.
Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997 Mar 1;25(5):955-64.
Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007;35(9):3100-8.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997 Sep 1;25(17):3389-402.
Chaudhuri RR, Loman NJ, Snyder LA, Bailey CM, Stekel DJ, Pallen MJ. xBASE2: a comprehensive resource for comparative bacterial genomics. Nucleic Acids Res. 2008 Jan;36(Database issue):D543-6.
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, et al. Versatile and open software for comparing large genomes. Genome Biol. 2004;5(2):R12.

Contact

For questions or comments about this service, please contact n.j.loman@bham.ac.uk.