bioinf http://bioinf.scmb.uq.edu.au/ 2026-04-20T10:10:21+00:00 bioinf http://bioinf.scmb.uq.edu.au/ http://bioinf.scmb.uq.edu.au/lib/tpl/bootstrap3/images/favicon.ico text/html 2018-07-04T07:22:12+00:00 Anonymous (anonymous@undisclosed.example.com) discord http://bioinf.scmb.uq.edu.au/discord?rev=1530652932&do=diff Expression vs. repression discordance An example Python source code to calculate the discordance score is provided [here] 'discordance.py' can be run with a command line tool. e.g. >>> python discordance.py -i example_input.txt -o output.txt -s hg19 text/html 2020-08-13T01:34:12+00:00 Anonymous (anonymous@undisclosed.example.com) evolusec http://bioinf.scmb.uq.edu.au/evolusec?rev=1597246452&do=diff Evolu-sec package <html> <p class=MsoNormal style='text-align:justify;text-justify:inter-ideograph'><span class=SpellE><span lang=EN-GB>Evolu</span></span><span lang=EN-GB>-sec package forms part of a research project, reported in “Evolutionary model of protein secondary structure capable of revealing new biological relationships”.<o:p></o:p><a href=" text/html 2021-09-20T17:03:39+00:00 Anonymous (anonymous@undisclosed.example.com) projects http://bioinf.scmb.uq.edu.au/projects?rev=1632121419&do=diff Research projects with the Boden group Informal collection of project ideas, at different levels and duration. Phylogenetics, ancestor sequence reconstruction, protein engineering, bioeconomy All biological components that are genetically encoded are subject to evolution—selective pressures in their ecological niche. With biochemists and protein engineers, we develop (phylogenetic) tools for detecting what specific changes explain the make-up of a gene or protein; this leads to a fundamental … text/html 2022-07-01T17:34:24+00:00 Anonymous (anonymous@undisclosed.example.com) seqscrub http://bioinf.scmb.uq.edu.au/seqscrub?rev=1656660864&do=diff SeqScrub is a web tool that cleans up FASTA files and associated phylogenetic tree files by removing unnecessary information while retaining unique IDs. SeqScrub can be accessed via the following link - SeqScrub The full code (JavaScript, PHP, and HTML) can be found at the following repo - text/html 2017-05-03T13:54:22+00:00 Anonymous (anonymous@undisclosed.example.com) sidebar http://bioinf.scmb.uq.edu.au/sidebar?rev=1493783662&do=diff * Research * Internal * Compute/Server * Education (Wiki) text/html 2023-07-27T18:21:25+00:00 Anonymous (anonymous@undisclosed.example.com) start http://bioinf.scmb.uq.edu.au/start?rev=1690446085&do=diff Bioinformatics portal Welcome to the bioinformatics portal, hosted by Boden lab. Web services * GRASP * T-Gene * STRViper * Evolu-sec-package * SeqScrub * Expression vs. repression discordance Sites * Research * Internal * Compute/Server * Education (Wiki) Authors text/html 2018-03-20T09:48:46+00:00 Anonymous (anonymous@undisclosed.example.com) strviper http://bioinf.scmb.uq.edu.au/strviper?rev=1521499726&do=diff STRViper: Short Tandem Repeat Variation Identification from Paired-End Reads Introduction STRViper is a bioinformatics tool for detection of short tandem repeat (STR) variations from paired-end next generation sequencing data. STRViper makes variant calls based on deviations in sequence fragment sizes, allowing the analysis of repeats of size up to the fragment length. This strategy also helps avoiding false calls resulting from errors that arose from repetitive DNA.