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TSSer
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Enables the automatic inference of transcription start sites (TSSs) from dRNA-seq data. TSSer allows the discovery of TSSs that may not be expected or easily evaluated such as those of antisense transcripts, alternative TSSs and TSSs corresponding to novel genes. This method can provide an initial set of high-confidence TSSs that can be used to train more complex models of transcription regulation, which could be used to iteratively identify additional TSSs, that may be supported by a small number of reads.
TSSAR
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(1)
Predicts bacterial transcription start sites (TSSs) from dRNA-seq data. TSSAR is a tool for automated de novo TSS annotation that respects the statistics of dRNA-seq libraries. It is built on a RESTful Client/Server architecture that allows for rapid screening and processing of Next-Generation Sequencing (NGS) data. The RESTful architecture of this tool provides additional extensibility, rendering implementation of new functionality such as promoter or operon characterization straightforward.
dRNA mapper
Obsolete
Detects degradome (d)RNA products derived from input genes. dRNA mapper is part of SoMART, the Server for plant miRNA/tasiRNA Analysis Resources and Tools. dRNA mapper provides experimental evidence for sRNA-directed cleavage by mapping dRNA reads to an input target sequence. As input, it uses a FASTA format sequence of the gene of interest and a selection of dRNAdb database from the pull-down menu. The background script uses BLASTN to query the input sequence against the selected dRNAdb(s) using default BLASTN settings, and reports the matching dRNA reads in a table. It also creates a dRNA read map of the input transcript at single-nucleotide resolution, and reports the data in a three-column table. Using this table, a chart can be created in Excel to show the distribution of the dRNA reads on the transcript.
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