Bioinformatics and the Cell: Modern Computational Approaches by Xuhua Xia

By Xuhua Xia

The various books which were released on bioinformatics have a tendency towards both of 2 extremes: those who function computational info with loads of arithmetic, for computational scientists and mathematicians; and people who deal with bioinformatics as a tremendous black field, for biologists. this can be the 1st publication utilizing complete numerical representation of mathematical recommendations and computational algorithms utilized in bioinformatics that converts molecular facts into prepared organic wisdom.

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Additional info for Bioinformatics and the Cell: Modern Computational Approaches in Genomics, Proteomics and Transcriptomics

Example text

Second, the nucleotide A at site 9 of S1 is now interpreted as homologous to the nucleotide A at site 10 of S2. Which of the two alignments makes more sense? If Alignment 1 is correct but we used a nucleotide-based alignment method and end up with Alignment 2, then the estimation of the genetic distance between the two sequences will be biased. The genetic distance measures the evolutionary dissimilarity between two sequences, often estimated by ignoring the indel sites. It is often used as an index of sequence divergence time in molecular phylogenetics, when calibrated by fossils with known divergence time.

6) when he was discussing man’s relationship to others: “This subject brings me to that vilest offspring of the herd mind - the odious militia. The man who enjoys marching in line and file to the strains of music falls below my contempt; he received his great brain by mistake - the spinal cord would have been amply sufficient. This heroism at command, this senseless violence, this accursed bombast of patriotism - how intensely I despise them! ” Yet in spite of Einstein’s antiwar stance, his successes have often been depicted with military analogies, such as how the established castles of physics came tumbling down at the trumpet of his theory of relativity, as if Einstein is a military general bent on conquering.

2-6). It is generally true that amino acids of different polarity rarely replace each other (Xia and Li, 1998), whereas amino acids with similar polarity can replace each other quite frequently (Xia and Kumar, 2006). Hb-A: Val-His-Leu-Thr-Pro-Glu-Glu…… Hb-S: Val-His-Leu-Thr-Pro-Val-Glu…… Figure 2-6. Sickle-cell anemia is caused by a single amino acid replace of a glutamate residue at the sixth position (Hb-A allele) by a valine residue (Hb-S allele). The mutant deformed hemoglobin molecules distort the red blood cell which progresses from the normal disk-like shape to the sickle-like shape.

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