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miRPV: An automated pipeline for miRNA Prediction and Validation in si
miRPV is an Automated tool that allows users to predict and validate microRNA from genome/gene sequence.
System Requirement
CPU: AMD64 (64bit)
Memory: 2Gb RAM
Storage: 5Gb
Ubuntu 18.04
A Custom Sequence Locus Typer for Classifying Microbial Genotypic and Phenotypic Attributes.
Publication:
Brinkac LM, Beck E, Inman J, Venepally P, Fouts DE, Sutton G. LOCUST: A Custom Sequence Locus Typer for Classifying Microbial Isolates. Bioinformatics (Oxford, England). 2017 Jan 27;
https://www.ncbi.nlm.nih.gov/pubmed/28130240
parastructure is a perl script collection to run the population genetics software STRUCTURE from Pritchard et al. 2000 (http://pritch.bsd.uchicago.edu/structure.html) in parallel on a cluster (beowulf type). Each run of K (the number of populations) is executed separately on each CPU of the cluster trough queue system based on PBS.
A summary statistics table and distruct figures (Noah Rosenberg: http://www.stanford.edu/group/rosenberglab/distruct.html) are built at the end of the run.
A patch...
Population simulator to solve next generation sequencing questions
Pop-seq is a perl based simulation tool, for generating any kind of mapping population using an user defined recombination landscapes. Combined with the Seq-sim tool you can generate pooled or bar-coded next generation sequencing biased outcomes. This tool were used to solve reappearing question in a experimental design (e. g. of how many plants or sequencing depth is advisable in a back crossed or out crossed scenario )
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CPU Balance is a Perl script to balance the CPU usage among users. It will allocate CPU resource to each user equally only by the command renice, no matter how many processes/threads a user runs.
################
# Basic Renice Goal
################
1. User-based balance: every user get the same cpu percentage if they ask for more;
2. all the jobs of one user has the same NI;
3. NI of all jobs tend to move as large as possible when balanced;
4. No sudden change on NI. max change of NI...
Development and support of OCFA have been discontinued. the code has moved to these github repositories:
https://github.com/DNPA/OcfaLib
https://github.com/DNPA/OcfaArch
https://github.com/DNPA/OcfaJavaLib
https://github.com/DNPA/OcfaModules
https://github.com/DNPA/OcfaDoc
If you are interested in contributing to ongoing work on the creation of a community maintained OCFA inspired computer forensic framework, please join the Mattock/MattockFS community page on G+:
https://plus.google.com...
RAPD Primer Design from Metagenomes (RPD-M) scans metagenome sequences identifying and determining relative frequency of candidate primers for Random Amplification of Polymorphic DNA (RAPD) assays.