RFLP Planner RFLP Planner - Find restriction enzymes that help differ known homologe DNA sequences
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RFLP Planner Tags

find simulate mutation find mutation electrophoresis simulation find restriction enzime

RFLP Planner Description

RFLP Planner - Find restriction enzymes that help differ known homologe DNA sequences RFLP Planner is an open source app that will help you plan an RFLP experiment: it finds restriction enzymes that cut a set of homologue DNA sequences in different ways and simulates the resulting gel- electrophoresis image. RFLP Planner should be platform independent, but is tested only on Mac OS X. helps you to find the crucial restriction enzymes that characterize the population.With the electrophoresis simulation it is easy to chose the restriction enzymes that show the best polymorphism on the gel.An important keyword is biodiversity. The program is written in Perl, uses some modules of BioPerl and the GD-Library. RFLP Planner should be platform independent, but is tested only on Mac OS X.Here are some key features of "RFLP Planner":· Simulation of gelimages (PNG): Every sequence one image. Every image with a molecular weight marker. Every restriction enzyme one slot.· Evaluation is done with the whole bioperl restriction enzyme database, but desired enzymes also can be added (EnzymeNAME or RESTRICTION^SITE)· Isoshizomers are not used for calculations (but appear in the resulting fragments.txt)· Sequences can be trimmed to the same lenght or not, but for the gelimage the original sequences are used· Desired molecular weight marker bands can be labelled· Option to label images (with sequence name)· Lots of different in- and output formats are supported (bioperl)· Abuse the program to cut primer sequences of a bunch of sequences: 1. in one sequence cut primer sequence manually 2. import all sequences (fasta) 3. choose: trimm = 1, aligned_format = 'fasta'· Automatic remove bad aligning sequences· Chose range of searched restriction enzymes (4, 6, .. -bp cutter)· Automatic reverse complement sequences (does not work for large amount of seq; if it does not work try with fewer sequences, exoprt alignment in fasta, join all sequences again, calculate the whole)

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