Bioinformatics: Dot Matrix or Diagram method explaned #1

One way to visualize the similarity between two protein or nucleic acid sequences is to use a similarity matrix, known as a dot plot. These were introduced by Gibbs and McIntyre in 1970 and are two-dimensional matrices that have the sequences of the proteins being compared along the vertical and horizontal axes. For a simple visual representation of the similarity between two sequences, individual cells in the matrix can be shaded black if residues are identical, so that matching sequence segments appear as runs of diagonal lines across the matrix.
Some idea of the similarity of the two sequences can be gleaned from the number and length of matching segments shown in the matrix. Identical proteins will obviously have a diagonal line in the center of the matrix. Insertions and deletions between sequences give rise to disruptions in this diagonal. Regions of local similarity or repetitive sequences give rise to further diagonal matches in addition to the central diagonal. Because of the limited protein alphabet, many matching sequence segments may simply have arisen by chance. One way of reducing this noise is to only shade runs or 'tuples' of residues, e.g. a tuple of 3 corresponds to three residues in a row. This is effective because the probability of matching three residues in a row by chance is much lower than single-residue matches.
Dot plots are one of the oldest ways of comparing two sequences.They compare two sequences by organizing one sequence on the x-axis, and another on the y-axis, of a plot. When the residues of both sequences match at the same location on the plot, a dot is drawn at the corresponding position. Note, that the sequences can be written backwards or forwards, however the sequences on both axes must be written in the same direction. Also note, that the direction of the sequences on the axes will determine the direction of the line on the dot plot. Once the dots have been plotted, they will combine to form lines. The closeness of the sequences in similarity will determine how close the diagonal line is to what a graph showing a curve demonstrating a direct relationship is. This relationship is affected by certain sequence features such as frame shifts, direct repeats, and inverted repeats. Frame shifts include insertions, deletions, and mutations. The presence of one of these features, or the presence of multiple features, will cause for multiple lines to be plotted in a various possibility of configurations, depending on the features present in the sequences. A feature that will cause a very different result on the dot plot is the presence of low-complexity region/regions. Low-complexity regions are regions in the sequence with only a few amino acids, which in turn, causes redundancy within that small or limited region. These regions are typically found around the diagonal, and may or may not have a square in the middle of the dot plot.

[@mohammedebrieeshetie790]

I DREAMED TO LEARN AGAIN . NOW THE WAY I UNDERSTAND THINGS HAVE A BIG AND BIG DIFFERENCE

[@middlevoids]

Thank u, Nikolay :3

[@ChrisBBloe]

Thanks so much

[@gabrielaraujogd]

Thanks a lot, greetings from 🇧🇷

[@GeneticsLessons]

You are welcome!

[@Bioinfowithwafa]

Very amzing

[@ericwuluglayjr6060]

Thanks a lot 🙏

[@GeneticsLessons]

You're most welcome

[@leon.frisch7446]

Awesome video my friend, also, your english is quite pristine!

[@GeneticsLessons]

Thanks! 😃

[@farahroaster9229]

If we do not put dots we put number like 1 2 3? Is it ok

[@GeneticsLessons]

Watch my new video - How to balance centrifuge without "dummy" tubes ruclips.net/video/iQz6mUeFcHE/видео.html

[@tejasrinivasulu283]

Thank you 😊

[@GeneticsLessons]

You're welcome 😊

[@nikhilv6456]

thank you so much sir was a great video i understood it very well

[@GeneticsLessons]

Watch my new video: How therapeutic anticancer vaccines are produced? ruclips.net/user/shorts8JSq4x-1htM

[@mohdsalim3295]

how this method can be used in marking and grading?

[@GeneticsLessons]

Watch my new short: How inbred was Adolf Hitler? ruclips.net/user/shortsVnq91tyFFR4

[@alaaaref3131]

thank you

[@GeneticsLessons]

You're welcome

[@AbuFatimahCS]

What is the difference between homology and similarity? I guess here you mean similarity.

[@GeneticsLessons]

Yes, if genes from different organisms or different genes from the same organisms but that represent "family of genes" with high degree of similarity we would call "similar".

[@sinikiwedlamini3004]

Thank you, this is really helpful

[@GeneticsLessons]

You're welcome!

[@danieltavares345]

shit bro you are amazing

[@aqwerzerd]

يا ناااااااااس مش عارف الم المادة

[@GeneticsLessons]

Watch my new short video How tardigrades may help biotechnology? ruclips.net/user/shortsP194Jt-LY_8

[@asianman1441]

Is this video legit? I can't tell anymore.

[@GeneticsLessons]

These Dot Matrix principles does not change with the time.