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 algor

SUBMITTER: Liang C 

PROVIDER: S-EPMC2789075 | biostudies-literature | 2009 Nov

REPOSITORIES: biostudies-literature