ArticleBMC bioinformatics2009
JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed.
- The drug-minded protein interaction database (DrumPID) for efficient target analysis and drug development.Database : the journal of biological databases and curation · 2016Article
- MaxSSmap: a GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence.BMC genomics · 2014Article
- Marine metagenomics: new tools for the study and exploitation of marine microbial metabolism.Marine drugs · 2010Review
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7 authors.
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Abstract
backgroundESTs 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.
resultsThe 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.
conclusionRapid prokaryotic EST mapping or mapping of sequence reads is achieved applying JANE even without knowing the cognate genome sequence.
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