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Bioinformatics

The tmRNA Website

Image Title The tmRNA Website.


Page Contact
Kelly Williams

(925) 294-4730


Corey Hudson

(925) 294-1575


Related Links
Sandia Biology

SOFTWARE

Genome Assembly Tools
readStepper.pl (Published name: extendFromReads.pl; citation: Hudson et al 2014 [Supp Matls]) This script takes an Illumina read set and a short query, and performs a grep-trim-sort. Despite its simplicity it produces a powerful visualization of the matching reads, with multiple "horns" when the query is repeated in the genome. We find this very useful for resolving assembly problems.
extendMulti.pl
getMates.pl
denovo.pl
indexReads.pl


Islander Genomic Island Identification Suite
Islander.tgz


Juxtaposer: Software to detect single-strain mobile events in bacteria
juxtaposer.tgz - the software
toyJuxtaposer.tgz - sample inputs and outputs


tFind_1_4 - (tRNA and tmRNA finder)
    tFind uses a combination of existing tools: tRNAscan-SE (Lowe and Eddy, 1997), BRUCE (Laslett et al. 2002) and ARAGORN (Laslett and Canback, 2004) to find and evaluate tmRNA, as well as our program rFind.pl, which includes our full- and terminus-sequence tmRNA databases which it searches using BLASTN. rFind.pl is directly used in this pipeline to find additional two-piece tmRNAs and accurately determine their termini and odd one-piece tmRNAs. These four programs are packaged together in tFind_1_4.tgz.

RapTOR, v2.0: pathogen detection in clinical samples through high-throughput sequencing

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