 Dear students, in this module I am going to introduce you to pairwise sequence alignment. This will be the first module in a series of three modules and I am going to introduce you to the concept of pairwise sequence alignment in this module. You already know that there are two types of matches when you are trying to compare to biological sequences. Exact matches are when you have two sequences and they are matching with each other, amino acid by amino acid or nucleotide by nucleotide and that they are in the exact same order. So in this way you can obtain an exact match. However what if you have two sequences which do not have an exact match with each other which actually is the majority of the cases that you will encounter. In such a case you can employ inexact matching and in inexact matching you can consider variations, differences between the sequences. Let's take a look at the pro side patterns again. So pro side patterns they allow you to build templates for inexact matching. So let's take a look at this pattern again. So this is from your textbook chapter 3 page 44. So these are the amino acids as you already know now while X represents any amino acid from the 20 amino acids. Essentially when you have an X anywhere in the pro side pattern it means you can place any amino acid here. I've circled all X's for you. Next the bracketed numbers they denote the repeat length of a residue. So for instance here you had an X right so you can have any amino acid here and that it should be repeated 10 times. So there are 10 amino acids that are here between F and R. In this way you can fill up the area between these two amino acids. Next there can be a case where this repeat length varies. As we just saw in this case the repeat length was just 10. So you could have 10 amino acids that were repeated. Here a little down in the sequence you can see 72 comma 86. So it essentially means any amino acid because there is an X here. It can occur between 72 to 86 times between E and R. So this is how pro side patterns are built and that they are very useful in generalizing the patterns within the sequences. Just to remind you this pro side pattern is for the map kinase which is a very very important protein in the cellular life. So all the proteins in the Swiss broad database which are of map kinase they follow this pro side pattern. Okay so let's move on. So to introduce you to the topic of pairwise sequence alignment you need to have you need to identify conserved sequences or unchanged sequences or amino acids within the overall sequence. To begin with you need to check for each amino acid in the corresponding sequence and see if there is a change or they are conserved. So this process involves in exact matching or considering mismatches while matching the overall sequence. Therefore this process is called alignment. So you have two sequences that align against each other and you're doing it in an in exact way therefore accommodating certain changes within the certain differences within the sequences. So pairwise would mean you have two sequences which you are trying to compare. So pairwise sequence alignment will be sequence alignment between two sequences. Two examples are given here for you. So as you can see in the first example this is sequence one this is sequence two so this is a pairwise alignment and that all the amino acids they match each other very nicely. So you have a lot of similarity between these two sequences. However in the example given below you can see that everything is matching except this portion. So because these two amino acids could not be found in the upper sequence so we have represented them with two dots here. The rest of the sequence matches very nicely. So these dots are called gaps and we'll talk about them in detail later. So in conclusion the pairwise sequence alignment allows you to compare two sequences against each other and that it is an inexact matching process and lastly as we just saw in the second example of the alignment if some amino acids or nucleotides are not present in the other sequence then you represent them by placing a dot in this called a gap.