Home My Page Projects Code Snippets Project Openings

Tag Cloud


Android C C++ Data Mining ESUP Esup-Commons Experiments Git JSF Java Linux MATLAB MTGAUE Markov Decision Processes Matlab Neuroscience ODF Octave OpenMP PHP Perl Primer Python Python3 R Satellite Image Time Series Scilab Script Simulation Simulink TEI TEI. WIMS XML XSLT acquisition affiche planning algorithm alignment analyse texte annuaire astronomie astrophysics astrophysique auth bash bibliotheque bibliotheques bioinformatics bioinformatique c c++ calcul scientifique calendrier climate cmake cnrs comparative genomics computer science controle crb data data analysis data mining data processing database django e-education editeur editeurs editor environment esup exercices interactifs file formations framework genetics gestion git hydrologie ical ics image processing inventaire isotopic pattern java javascript jsonrpc k-mers lamp library linguistique logging mapping mass spectrometry mathematics matlab mission model modelisation monitoring mudslide pedagogie peptide permutation method php pl portlet postgresql protein proteomics python python3 qooxdoo qt5 quality quality alignment quantification read recommender systems satellite optical images script scripting scripts security sequencing signal processing simulation spectrum statistical tests statistics statistiques toolbox unitary events user friendly visualisation web wordpress workflow zone critique
2 projects in result set.
isbpFinder - isbpFinder is a Perl script dedicated to design ISBP (Insertion Site Based Polymorphism) markers. It allows the creation of features representing primers/amplicons covering the junction between 2 transposable elements (TEs) in order to obtain a graphical view of the different markers designed by viewing the feartures through a sequence annotation software such as "Artemis". isbpFinder can generate output files in CSV, EMBL and GFF format containing TEs and amplicons/primers. IsbpFinder is based on the following programs: - "RepeatMasker" for TE detection - "Primer3" for primer design for TE junction amplification. For more details about ISBP markers, please read "Paux et al., Plant Biotechnology Journal 2010(8):196-210" ( [url=http://www.ncbi.nlm.nih.gov/pubmed/20078842]test[/url] )
Tags: ISBP, Primer, TE, Perl
This project has not yet categorized itself in the Trove Software Map


Activity Percentile: 0
Activity Ranking: 0
Registered: 2015-06-03 16:00

ssrFinder - ssrFinder.pl is used to develop Simple Sequence Repeat (SSR) markers from a list of query DNA sequences provided in FASTA format. It uses a regular expression to identify all SSR motifs along the input sequences. Any tract of repetitive DNA in which a k-mer of length k repeated at least n times will be labeled as a potential SSR marker: k=1, n>=12 ex: AAAAAAAAAAAA k=2, n>=6 ex: ATATATATATAT k=3, n>=4 ex: ATCATCATCATC k=4, n>=3 ex: ATCGATCGATCG For each SSR identified in the list of query sequences, the script is able to design a pair of primers located on each side of the repeated motif. These primer sequences can then be used for DNA amplification by Polymerase Chain Reaction (PCR).
Tags: Primer, SSR, Perl
This project has not yet categorized itself in the Trove Software Map


Activity Percentile: 0
Activity Ranking: 0
Registered: 2015-06-03 15:50