This tutorial explains the use of Gustavo Glusman's BioMOO sequence aligner.

The sequence aligner is used for some of the exercises on dynamic programming in the "Pairwise Sequence Alignment" chapter of our BioComputing Hypertext Coursebook.

Table of Contents.

  1. Creating an aligner.
  2. Using the Web interface.
  3. Examples.

Creating an aligner.

You can use the aligner that's locked in the Alignment room, but it might lead to confusion if multiple people are accessing it simultaneously. It is therefore advisable to create your own.

To create your own aligner, connect to BioMOO, request a character/User-Id (if you havn't done that already), and type 


@create #306 named Fred
The MOO responds approximately as follows: 

You now have Fred with object number #4875 and parent generic two-sequence 
aligner (#306).
(where #306 is the object number of the Aligner you are creating another instance of, and Fred is the name you are giving it. #306 is a reference to the BioMOO implementation of a sequence alignment tool based on dynamic programming.) Note the object number (#4875 in this case); if you forget it, you can type 
@audit me
to query the MOO. You don't need to worry about removing your aligner later on; it doesn't need much disc-space.

By default, the aligner will be noisy. Every time it's used everyone in the room will be notified of what action was performed and the result. The purpose of this is to allow the instructors to know what the students are doing, but if there is more than one aligner in your room it could get very confusing. For this reason the following command could be useful: hush Fred. To make the aligner noisy again use: noise Fred.

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Using the Web interface

If you know the object number of your aligner, you can directly access it by pointing your browser (MUST BE Mosaic 2.5, or Netscape !) at: http://bioinfo.weizmann.ac.il:8000/32/view/XXX, where XXX is the object number. Maybe you're now prompted for your BioMOO UserId ("Character"), and your BioMOO password. You will be presented with a fill-in form.

In this form you will enter your sequences and select the costs matrix you need. Currrently only Levenshtein is supported. The [Update info] button changes the form's matrix to reflect your data.

You don't need to care about the "Zero first sequence" and "Zero second sequence" options right now; these implement a variant of the simple alignment presented here, which is discussed under the heading "Local Alignment" in our "Pairwise Sequence Alignment" chapter.

Now you can fill the matrix by clicking on a cell that is the intersection of the positions in each sequence that you are interested in. For example: if the matrix is 5x5, and you click on position (2,3), a new form will be returned that has the positions (1,1) thru (2,3) filled in and the rest zeroed.

The [Do alignment] button returns the matrix you filled in, the "traceback path", and the result of the alignment, but only up to the positions you selected via the matrix.

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A few examples

Here's an example illustrating the use of the Sequence Aligner.

Example 1

Let's start with the example given in Chapter 1 of the text. (In the section about Calculating Edit Distances).

Given the two sequences AGCACACA and ACACACTA, let's use the sequence aligner to compute the optimal alignment.

We will use the Levenshtein costs matrix.
Enter the two sequences and hit the [Update info] button.

By clicking in the matrix we can explore the alignment of parts of the sequences.

Here we clicked on position (5,3), and here

we clicked on (3,5).

Note that the first sequence runs from top to bottom, and the second sequence runs across, just like it's done in the coursetext, where s runs from top to bottom, and t runs across. That's why the pair (5,3) corresponds to ``fifth column, third row''.

If we want to see the optimal alignment for what we have selected, we simply need to hit the [Do alignment] button.

Here, the Alignment is 

A-GC-
|
ACACA
Note that the symbols ``-'' (and ``|'') in the matrix symbolize the introduction of gaps, whereas ``\'' denotes a replacement or match. The first ``\'' here denotes the match of the first ``A'' in the first sequence with the first ``A'' in the second sequence; the second ``\'' denotes the replacement of ``G'' in the first one by ``A'' in the second one.

Let's say we are interested in the alignment of the complete sequences. Click on element (8,8) of the grid.

All the positions are now filled in. To calculate the alignment hit [Do alignment]

Voila! The optimal alignment!

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Go to the BioMOO Home Page
Basic MOO Commands
16 May 1995
Chris Perreault

Back to VSNS BioComputing Division Home Page.
VSNS-BCD Copyright 1995.
Edited by Georg Fuellen