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Displaying results 1-2 out of 2 total.

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
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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
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Registered: 2015-06-03 15:50