title: JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes.
abstract: 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.
  
  
  CONCLUSIONS
  Rapid prokaryotic EST mapping or mapping of sequence reads is achieved applying JANE even without knowing the cognate genome sequence.
authors: Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany. liang@biozentrum.uni-wuerzburg.de
authors: Chunguang
authors: C
authors: Liang
authors: Alexander
authors: A
authors: Schmid
authors: María José
authors: MJ
authors: López-Sánchez
authors: Andres
authors: A
authors: Moya
authors: Roy
authors: R
authors: Gross
authors: Jörg
authors: J
authors: Bernhardt
authors: Thomas
authors: T
authors: Dandekar
mesh_terms: D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D016678:Genome; D020407:Internet; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface