JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes.

BMC Bioinformatics
Chunguang LiangThomas Dandekar

Abstract

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. 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. Rapid prokaryotic EST mappi...Continue Reading

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Citations

Apr 9, 2016·Database : the Journal of Biological Databases and Curation·Meik KunzThomas Dandekar

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Datasets Mentioned

BETA
CP000770
CU207366
CP000046
AE015929

Methods Mentioned

BETA
single cell sequencing
454 sequencing

Software Mentioned

Apache
Perl scripts
Cap3
phrap package
linux
JANE ( Just Analyze Nucleotides and ESTs )
Exonerate
JANE
Perl
Phrap

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