Blog of Andrés Aravena

5. Existence/extension?

09 November 2022

The biological reason for affine gaps is that indel initiation is hard, but once it exist, extensions are easy. In other words, nature prefer few long gaps instead of many short ones.

Student 1 50

Existence is represents the initial gap while extension represents the external gap, in other words, the length. Gap score is the sum of these values because they both represents the differences between sequences.

Student 2 40

We called these affine gaps. cost= (initial cost (or) existence) + length . extension

While calculating this cost small expected value should be chosen because it may be biologically meaningful. The value gives us an idea about the biological similarity of the sequences that we are comparing. When the extension has larger score, threshold gives less hits. Because while jumping in the sequence and adding gaps, it’s not make sense to jump small/a lot. Jumping once requires less effort and penalized less. To be clear a lot of small gaps in a large sequence decreases the understanding biological purpose. If we jump large, then we can localize the sequences seperately and have more sensitive and biologically sensitive results.

Student 3 90

It’s because of affine gaps. And because, in nature and biology the first gap is expensive but the consecutive gaps are cheep. So we prefer "A _ _ _ TC" to "A _ T _ C _ " in biology. It is expensive to add a gap in every time, it increases the existence. If we add all the gaps at the same time, it decreases the existence we only pay for extensions for the gap length.

Student 4 100

If the gap score have two parts: existence and extension, that’s name is Affine gaps. Existence means gap opening penalty. We want to have similar sequences, so if there is a gap opening this means similarity begins to disintegrate, so there is a penalty for it. For the length of gap, the penalty is given by extension. We do not want sequences that have short length but several gaps, we prefer to see one gap with long length.

Student 5 40

Existence is meaning of gap opening, it shows us the part of the sequences that they matched. Extension is meaning of gap cost and shows us doesn’t match. The biological reason is gaps values must reflect how real insertions and deletions occur in nature, so this gap scores show us the similarity about two sequences as nucleotide or aminoacids.

Student 6 100

We have to calculate penalty in alignments. Sometimes our alignment has few gaps. So we calculate the costs to think about existence and extension. Existence is gap opening cost. Extension is gap cost and its cheaper than existences cost. So it shows that which alignment is more biological. We want few long gaps(more biological) instead of many short gaps.

Student 7 100

Gap values reflect how real insertions and deletions occur in nature. We observe that, once an indel event starts, it can easily grow. If the polymerase jumps, then it can jump a long distance. Therefore the first gap is expensive but consecutive is cheap. It is called Affine Gaps.

Student 8 50

existence is a cost caused by the initial gap, depending on as biological insertion, deletion or mutation.. Extension is a caused by the length , by meaning the frequency of presence gap or accumulated gaps together. It could be caused during dna replication. DNA polymerase could jump and cause some gaps.

Student 9 100

These kinds of gaps are called affine gaps. The reason they occur is how polymerase behaves—once it jumps it becomes easier or more possible for it to jump once again. Thus, we have two scores called existence, which is the initial gap penalty, and extension, which is the gap extension penalty.

Student 10 100

Existence is initial gaps and extension gaps are other gaps. DNA poly. enzymes prefer to jump single gap or many gaps whereas it does not prefer to jump every time. for example

- A-B-C-D ( not like this )    -A - - -BCD (like this).

Student 11 50

Existence is the cost of having a gap, extension is the penalty for extending a gap.

Student 12 100

If we consider DNA polymerase’s function ,as an example, this enzyme does not tend to jump. For this reason, first gap,which we call it existence, must has high cost. But once it jumps, it can easily grow. So, other gaps, after the first one, which we called extension, must be cheaper.

Student 13 50

Affine gaps; first gap is expensive but the consecutive are cheap.

Student 14 100

Existence is the cost of having a gap, extention is the cost of consecutive gaps. If the polymerase jumps once, it can jump a long distance that is why extension is cheaper.