Dotplot plotting

Dot plot is a graphical method that allows the comparison of two biological sequences and identify regions of close similarity between them.
Introduction 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. It can be seen from Figures 3.3h,c that the number of diagonal runs in the matrix has been considerably reduced by looking for 2-tuples or 3-tuples.

Python for bioinformatics

Breakthrough cancer research studies DNA

Scientists say they have found dozens of DNA markers that could help predict a person's risk of developing certain types of cancer. It means tests could be used to find people at greatest risk and help them take preventative action.

Introduction to Bioinformatics

Biochemistry Lecture (Protein Purification)

Adrenogenital Syndrome

This condition is also more properly known as congenital adrenal hyperplasia. This is a group of conditions of similar source: a family of autosomal recessive disorders of steroid hormone production in the adrenal glands leading to a deficiency of cortisol, the stress fighting hormone. The master hormonal regulatory gland, the pituitary, sensing the deficiency, secretes massive amounts of the stimulating hormone corticotropin to bring the cortisol levels up to normal. This hormone in turn causes the adrenal glands to overproduce certain intermediary hormones which have testosterone-like effects on the fetus and child, leading to so-called "virilization."

Induction Apoptosis

Wildtype MEFs response to Nocodazole Video


New Cancer Drug Shrinks All Tumors

Calcium Signalling

Calcium is a common signaling mechanism, as once it enters the cytoplasm it exerts allosteric regulatory effect on many enzymes and proteins. Calcium can act in signal transduction after influx resulting from activation of ion channels or as a second messenger caused by indirect signal transduction pathways such as G protein-coupled receptors. video