Software for:
Making Restriction Maps
Designing PCR primers
Assembling fragments, detecting SNPs, and managing raw sequence data
For : GCG, Mac, PC, UNIX,
and on the Web
Restriction Mapping
-Making restriction maps was my first use of “Molecular Biology” software
-Making restriction maps is a routine lab activity that is necessary for any type of cloning project.
-High quality maps are important for publications and exchange of information between researchers or between labs.
Archiving Data
-Maps are a common way for labs to archive information about entire libraries of plasmid constructs.
-It is important that map data are stored in a reliable format so that the obsolescence of a particular computer program does not render archives unusable.
Mapping Software
-Programs vary greatly in sophistication and ease of use
-Simple drawing programs (vector graphics)
-The venerable DNA Strider
-GCG (not a strong point of the package)
-Comprehensive Mac/PC MolBio programs
-Dedicated plasmid drawing programs
-Can it be done on the Web?
-Making high quality graphical restriction maps is one area where Mac/PC programs are much better than GCG or the Web
GCG Mapping ProgramsGCG has a full set of functional restriction mapping tools
This may be your best bet if you simply need to locate some restriction sites to plan a cloning project
MAP allows you to search for any enzyme site in REBASE
MAPPLOT makes a graphical output from MAP
MAPSORT simulates a restriction digest and predicts the sizes of digest products with any combination of enzymes
FINDPATTERNS allows you to search for short sequence patterns (enzyme sites, promoters, enhancers, etc.)
PLASMIDMAP is a GCG program that produces a "publication quality circular map" of a plasmid construct
(I know of no one who has ever successfully used this program)
Using MAP
MAP is the main GCG restriction mapping program. Like a lot of GCG programs, it is very powerful and quite complex.
-Restriction sites can be mapped for all enzymes (the default), or a set of enzymes that you specify by name
-You can also select just enzymes with 4, 5, or 6 base recognition sites; and 5’, 3’, or blunt end cutters
-You can allow a single base mismatch between the enzyme recognition site and your target sequence
-The output can be viewed as a linear map or in a table format
-MAP provides protein translations (in 3, 6, or any single reading frame)
Web Mapping Tools
There are some free mapping tools on the web for finding restriction sites and making text maps, but not for nice graphical maps
WebÇutter (Max Heiman, Yale Univ.)
http://www.firstmarket.com/cutter/cut2.html
EMBOSS Restrict (EMBL Institut Pasteur)
http:/http://www.bbioo.com/bioweb.pasteur.fr/seqanal/interfaces/restrict.htmlRestriction Maps (Colorado State Univ.)
http://arbl.cvmbs.colostate.edu/molkit/mapper/index.html (uses Java)
WebCutter
Webcutter is a free on-line tool to restriction map nucleotide sequence (text output)
http://www.firstmarket.com/cutter/cut2.html
Webcutter includes the option of finding restriction sites that can be introduced into a sequence by silent mutagenesis
EMBOSS Restrict
http:/http://www.bbioo.com/bioweb.pasteur.fr/seqanal/interfaces/restrict.html
A JAVA Program
http://arbl.cvmbs.colostate.edu/molkit/mapper/index.html
From R. A. Bowen at Colorado Sate University
JAVA applets displayed on a web page cannot be directly printed, can only grab screen shots - useless for publication
Mac & PC Mapping Programs
Restriction mapping is one of the simplest molecular biology computing tasks - many MolBio software packages provide this function:
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