Tutorial

This page provides a tutorial on using the MGAlign web service. The use of this web service is very straight forward, basically you submit a job consisting of a mRNA sequence and a Genomic sequence and a Results page is returned allowing for simple analysis. This is a step by step guide to using and interpretating the web service.

The various steps are as follows:

1. Entry of mRNA sequence
2. Entry of Genomic sequence
3. Submit job to server
4. View the results

Step 1. Entry of mRNA sequence.

You have to first provide a mRNA sequence. This can be done in two ways. The first is to copy the mRNA sequences from your text editor or sequence editor and paste it into the textbox provided in the "Use it" page as shown in the figure below. Alternatively you can select a FASTA format file from your computer by clicking the "Browse" button again shown in the below. Note that there is a 25,000 nucleotide limit on the mRNA sequence.

Step 2. Entry of Genomic sequence.

You then repeat this for the genomic sequence in the same manner as for the mRNA sequence as shown with the figure below. Note that there is a 250,000 nucleotide limit on the genomic sequence.

Step 3. Submit job to server.

Lastly you click on the "Do Alignment" button to submit the job to the server as shown below.

Step 4. View the results.

After the server has aligned the two sequences, you will be presented with a page similar to the one shown below.

The results page can be divided into three sections, the Top Menu Section, the Graphical View Section and the Details View Section. The easiest way to view the alignment of the exons is to click on the second row of colored bars which represent exons in the figure at the center of the results page. The easiest way to view the intron sequence is to click on the Splice Site Motifs in the figure. You can also obtain FASTA files of the introns and exons by clicking on the blue button with the text "FASTA file". More help on the various elements of the results page can be found here.