JaMBW - Reverse, Complement, Inverse

To use this tool, the URLs http://www.bioinformatics.org/ and http://virican.net must be added to the list of site exceptions in the 'Security' section of Java Settings installed in your Operating System. An alternative tool that does not require Java is available in this link.

A Java-enabled browser would have in this place a window similar to this picture:

Given a sequence of nucleic acids, this program generates its reverse, its complement, and its inverse into three independent windows. The above mentioned terminology is explained with the following example:

5' ATATATCCCGGCG 3' input sequence
5' GCGGCCCTATATA 3' its reverse
5' TATATAGGGCCGC 3' its complement
3' TATATAGGGCCGC 5' its inverse (say, reverse and complement) 

Mode of operation

This program uses 4 windows: the top one should be filled from the user, with a sequence of interest, while the other 3 windows contain the results of the operations. The following steps must be performed:

  1. Sequence input
    • Symbols used
      Either paste or type in the top area the sequence of interest. Any character or symbol that does not belong to the IUB [atcgATCG] set is ignored.
    • removal of header information
      Only the sequence must be placed in the top window: heading comments must be removed
    • long sequences and small window
      In order to allow users with small screens to still be able of using this program, the size of each window had been made rather small. Therefore, use the scroll-bars in order to move around in the input and output windows. The suggested strategy is to double click in the specified area and then do copy/paste from/to the text-editor of choice or across different applications.
  2. Case sensitivity choice
    Often is useful to mark regions of interest by changing the Case. This applet is capable of keeping those modifications also in its output, as well as to change the case of the sequence according to your wish. Therefore, by selecting anyone of the 3 choices provided, and hereafter described, the user has control on this aspect. In order to choose the case in the output, the following selections are possible, by clicking on the button close to them:
    • Unchanged, leaves the same case in the output as in the input, and is useful for easier identification of already marked regions in the sequence
    • Upper, generates as output the upper case conversion (e.g. atcg becomes ATCG)
    • Lower, generates as output the lower case conversion (e.g. ATCG becomes atcg)
  3. Convert
  4. Once the sequence is placed in the top window, by pressing the "CONVERT" button then the conversion is performed.

How to understand its output

Since both aim and mode of operation are rather straightforward, also the understanding and the use of the results from this work should not present any major difficulty. The output will simply consist of the same sequence reverse, complemented and inverted as in the examples shown above.

References

  1. Watson,J.D. and Crick,F.H.C.(1953) Genetical implications of the structure of deoxyribonucleic acid. Nature,171,964-967.
  2. Nomenclature Committee of the International Union of Biochemistry (NC-IUB) (1985) Nomenclature for incompletely specified bases in nucleic acid sequences. Recommendations 1984.Eur-J-Biochem,150,1-5

JaMBW Chapter 2.1 - Reverse, Complement, Inverse. Author: Luca I.G. TOLDO, Edition date: 28 February 1997. More information on JaMBW 1.1 in this paper