Tag: Tools

software  AnnotQTL website has been released!

Recently, we have released a new website: AnnotQTL, a web tool designed to gather the functional annotation of different prominent website though limiting the redundancy of information.

The last steps of genetic mapping research programs require to closely analyze several QTL regions to select candidate genes for further studies. Despite the existence of several websites (NCBI genome browser, Ensembl Browser and UCSC Genome browser) or web tools (Biomart, Galaxy) to achieve this task, the selection of candidate genes is still laborious. Indeed, information available on the prominent websites slightly differs in terms of gene prediction and functional annotation, and some other websites provide extra-information that researchers may want to use. Merging and comparing this information can be done manually for one QTL containing few genes but would be hardly possible for many different QTL regions and dozen of genes. Here we propose a web tool that, for the region of interest, merges the list of genes available in NCBI and Ensembl, removes redundancy, adds the functional annotation of different prominent web site and highlights the genes for which the functional annotation fits the biological function or diseases of interest. This tool is dedicated to sequenced livestock animal species (cattle, pig, chicken, and horse) and the dog as they have been extensively studied (indeed, more than 8000 QTL were detected).

The AnnotQTL server could be found here : http://annotqtl.genouest.org/

PERL  Control your jobs!

Let’s explain the situation: you have a lot of analyses to compute on your SMP computer (same analysis on different files, many different analyses or same analysis many times, for simulation purpose, for instance). And, for different reasons, you cannot use or you don’t have access to a cluster with many nodes… First, forget to launch job one by one and forget also to launch all the jobs in one command (since your server may go down)!

You can perform such tasks by writing csh scripts, which will control your jobs and fill the job queue. Maybe you can also install some queue manager on your server. By looking at the web, I didn’t find a “simple” way to solve this problem, so I wrote a simple PERL script, which manages a queue jobs list. This script is based on the Proc::Simple module (available here). The full documentation of this script is available here. Basically, you can choose between 3 analysis mode: many different analyses, same analysis on different input datafiles and same analysis many times. You also have to specify the number of simultaneous jobs to run (i.e. the number of available cpu) and the script will manage your queue job list. I’m not sure it’s the best way but it works for me.

I hope it will be useful and feel free to comment this article.

software  MarketSet

What is MarkerSet?

MarkerSet is a command-line tool designed for selection of marker panel(s) according to genomic location and known informativity on experimental crosses (e.g. for wide genome scan). MarkerSet can be used with either SNP or microsatellite markers, because it only relies on informativity data. Basically, the algorithm will select the most informative markers in two windows separated by a constant gap, and sliding on the genome. MarkerSet will define automatically the windows size and the gap distance between the two windows depending on the wished number of markers to select and genome size. MarkerSet has several options to optimize markers selection with the possibility to give more weight to the markers distances or to the markers informativity. In case of availability of several experimental designs, it is possible to compare the markers set quality obtained by selecting markers perfectly fitted for each experimental design (monodesign selection), or by selecting a set of markers common to all designs (multidesign selection).

MarkerSet is designed to be compatible with any kind of markers and species.

What do I need to run MarkerSet?

MarkerSet needs a functional PERL environment with POSIX module available (typically *nix system, may work with MacOS X). MarkerSet.pl and config.pm files must be installed in the same directory.

The input file must be a plain tabulated text file with the following informations (headers are requested):

Markers name – chromosome – genomic location – informativity values for cross 1 (typically the number of heterozygote founders) – informativity values for cross 2 …

The available download package comes with core files (PERL program and config file), README file for explanations on program parameters, example input files, and a verbose log file for a better understanding of the algorithm.

Source

To download the markerset package, click on the following link: markerset_package.tar.gz

The article about this software could be found at BMC research Notes and the INSTALL and USAGE documentation can be found here.