Find Restriction Map Software

Molecular biologists use a special class of enzymes, called restriction endonucleases, as a type of chemical scissors to DNA into pieces of manageable size. There are many different restriction enzymes, each of which cuts the DNA at a specific recognition sequence (a pattern of usually 4-8 nucleotide bases). For example, when the EcoRI restriction enzyme finds the bases "GAATTC" in a sequence, it cleaves the sequence between the G and the adjacent A. DNA ligases are then used to insert the resulting pieces into vectors, which make many copies of the inserts.

Researchers often want to know where their sequence of interest would be cut by various restriction enzymes. Various software packages and web tools are available for this type of sequence analysis.

Although NCBI offers a wide range of molecular biology databases and tools, it does not necessarily have tools to meet all user needs. Does NCBI have restriction map software? What is an easy way to find out? If not at NCBI, where can a user find restriction map software?

This exercise shows how to find the software by introducing some directories of molecular biology databases and software. (For an example of how to use restriction map software on a query DNA sequence, see the course module on DNA Analysis.) As you will see by searching the directories below, they vary in scope and interface. Some will have the type of software needed by the users while others will not, but a number of them are featured here so you can gain experience with the directories and find one or two that you like best.

Determine if NCBI has restriction mapping software or web tools

1. NCBI Resource Guide - see if the term "restriction" exists in the name or description of any NCBI resource



• use your browser's Edit/Find in Page function to see if the term restriction exists in the name or description of any NCBI resource
• because the Resource Guide is a catalog of NCBI resources, a key term such as "restriction" would be present in the name or description of a relevant resource
• if such a key term does not in the Resource Guide (as is the case), it indicates that NCBI probably does not have that type of resource
• you might want to search the NCBI web site (next step) to confirm this


2. NCBI Site Search - see if the term "restriction" or "restriction map" exists on other pages within the NCBI web site



• to confirm the results of the Resource Guide search, you can also do an NCBI site search for the term restriction (or restriction map). Either of those searches will retrieve a number of hits on the NCBI web site, but the context in which the search term appears will vary and none of the hits are for software or web tools that allow a user to create a restriction map of a query sequence. (The closest hit is to a restriction optical map entire of the Plasmodium falciparum genome, but not to a restriction mapping tool.)
• because NCBI does not offer a restriction mapping tool, search some directories of molecular biology databases and software, such as the examples listed below, to find sites that do.

Search some directories of molecular biology databases and software. Try each of the following and compare results. Some directories focus on either databases or software, while others contain a mixture of both, so you'll find hits in some and not in others.

1. Nucleic Acids Research 2007 Database issue -- published annually on January 1, the database issue features 3-5 page summary articles on over 100 databases each year. Because of the large number of databases in existence, each issue only covers a subset. There is also a companion searchable database of summary articles from current and previous database issues



• search the current Database issue and/or the database of summary articles for the term restriction (or restriction map)
• as is true for some of the other directories noted on this page, the NAR issue features databases rather than software, so a search for restriction will not necessarily find a hit relevant to this user's need


2. Nucleic Acids Research Web Server issue - launched on July 1, 2003 as a companion to the annual NAR Database Issue, focuses on web servers and analytical tools rather than molecular biology databases

   2003 Web Server editorial (full text); complete table of contents
   2004 Web Server editorial (full text); complete table of contents
   2005 Web Server editorial (full text); overview; complete table of contents
   2006 Web Server editorial (full text); overview; complete table of contents
   2007 Web Server editorial (full text); overview; complete table of contents
   Searchable database of web server summaries

• within each Web server issue table of contents, you can do an "edit/find in page" to search for the term restriction (or restriction map). Depending on the servers covered in each issue, you might find hits for one, both, or neither terms. For example, a search for "restriction" will find hits in the 2003 and 2007 table of contents (for NEBcutter and REPK, respectively), but a search for "restriction map" does not find any hits.
• alternatively, or in addition, search the complete set of database summaries for the term restriction (or restriction map). For example, as of August 3, 2007, a search for "restriction" will find 8 hits: DyNAVacS, FPC, REBASE, REPK, Software for MacOSX at Mek&Tosj.com, The SNP Consortium, WatCut, WebTraceMiner. For some reason, NEBcutter is not retreived by a search of the database summaries as of 8/3/07.



3. ExPASy Life Science Directory - originally developed by Amos Bairoch, Head of the SWISS-PROT group at the Swiss Institute of Bioinformatics, and now maintained by ExPASy



• use your browser's Edit/Find in Page function to see if the term restriction exists in the name or description of any resource on the page
• because the ExPASy page primarily lists molecular biology databases rather than software, you find some hits related to the former (e.g., REBASE - a database of restriction enzymes and methylases), but you don't find a restriction mapping tool
• near the top of the page, note there is a category for "Biol. soft. & db catalogs", so if you don't find something on the ExPASy page, just look further in the catalogs (some of which are included on this page)


4. Biocatalog by EBI - a catalog of molecular biology databases and software programs maintained by the European Bioinformatics Institute (EBI)



• browse the catalog by category, following the links for Mapping, then Restriction Maps. Use your browser's Edit/Find in Page function to find resources that contain the term restriction in their name or description.
• or search the Biocatalog using the Sequence Retrieval System (SRS) server:
• select the Library Page tab
• expand the Other Databases category
• check the box beside BIOCATAL
• enter restriction (or restriction map) as the search term
• press the Quick Search button beside the text box
• the search results page will display a list of database entry numbers that match your query. Use the Display Options dialog box in the left sidebar to display the complete entries.

Web Search

Of course, as an alternative to searching specific directories of molecular biology databases and software, you can do a general search of the web using a tool such as Google. In that case, it would be better to use a narrower search term such as "restriction map" (rather than just the word "restriction"). One advantage of searching directories such as the NAR Database and Web Server issues, however, is that the resources you will retrieve have been peer reviewed.