Software
JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes
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* Corresponding authors: Chunguang Liang liang@biozentrum.uni-wuerzburg.de - Thomas Dandekar dandekar@biozentrum.uni-wuerzburg.de
1 Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
2 Department of Evolutionary Genetics, Institut Cavanilles de Biodiversitat i Biologia Evolutiva, University of Valencia, Spain
3 Department of Microbiology, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
4 Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Jahnstrasse 15, 17487 Greifswald, Germany
5 EMBL, Postbox 102209, D-69012 Heidelberg, Germany
BMC Bioinformatics 2009, 10:391 doi:10.1186/1471-2105-10-391
Published: 29 November 2009Abstract
Background
ESTs or variable sequence reads can be available in prokaryotic studies well before a complete genome is known. Use cases include (i) transcriptome studies or (ii) single cell sequencing of bacteria. Without suitable software their further analysis and mapping would have to await finalization of the corresponding genome.
Results
The tool JANE rapidly maps ESTs or variable sequence reads in prokaryotic sequencing and transcriptome efforts to related template genomes. It provides an easy-to-use graphics interface for information retrieval and a toolkit for EST or nucleotide sequence function prediction. Furthermore, we developed for rapid mapping an enhanced sequence alignment algorithm which reassembles and evaluates high scoring pairs provided from the BLAST algorithm. Rapid assembly on and replacement of the template genome by sequence reads or mapped ESTs is achieved. This is illustrated (i) by data from Staphylococci as well as from a Blattabacteria sequencing effort, (ii) mapping single cell sequencing reads is shown for poribacteria to sister phylum representative Rhodopirellula Baltica SH1. The algorithm has been implemented in a web-server accessible at http://jane.bioapps.biozentrum.uni-wuerzburg.de webcite.
Conclusion
Rapid prokaryotic EST mapping or mapping of sequence reads is achieved applying JANE even without knowing the cognate genome sequence.