RFLP planner is a tool that helps to plan a RFLP experiment: It finds restriction enzymes that cut a set of homologue DNA sequences in different ways and simulates the resulting gel- electrophoresis image. The program 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.
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)
What's New in This Release:
· possibility to chose output folder where all files will be stored
· if writing files fails, message where else they are stored
· textfile with enzyme fragments has a nice "humanreadable" timestamp.
· enzyme fragments file is formatted now using spaces instead of tabs -> this makes it easier to read in text editor, but more difficult to inport to tables.