JaMBW Chapter 2.2

Randomize your sequence


Given a sequence (of nucleic acids or aminoacids), this program generates a new version of it consisting of the same symbols but in a randomized order. This is explained with the following example

TODAYISANICEDAY input sequence
SDEAAIDYOTIYACN output randomized order

Use of a randomized sequence is especially important when evaluating results of alignments (usually results of database searches) giving weak homologies. In such cases is "good practice" to perform subsequently a second search, but using a randomized version of the sequence and then compare the results obtained in the two runs.

Mode of operation

This program uses 2 windows: the top one should be filled from the user, with a sequence of interest, while the other window contains the result of the randomization. The following steps must be performed:

  1. Sequence input
  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 any one 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:
  3. Shuffle
    Once the sequence is placed in the top window, by pressing the "SHUFFLE" button then the conversion is performed.

A Java-enabled browser would have in this place something which looks like the following picture:

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. In fact, the output will consist of simply a sequence with the same composition as the input but in a fully unpredictable order.


  1. Doelz, R.(1990) BioCompanion, Biocomputing Essentials series, ISBN 3-905 434-00-8

Author:Luca I.G. TOLDO, Edition date: 28 February 1997