Blast by Ian Korf

By Ian Korf

Series similarity is a robust device for locating organic functionality. simply because the historical Greeks used comparative anatomy to appreciate the human physique and linguists used the Rosetta stone to decipher Egyptian hieroglyphs, at the present time we will be able to use comparative series research to appreciate genomes. BLAST (Basic neighborhood Alignment seek Tool), is a worldly software program package deal for fast looking of nucleotide and protein databases. it's essentially the most vital software program applications utilized in series research and bioinformatics. so much clients of BLAST, besides the fact that, seldom stream past the program's default parameters, and not make the most of its complete strength. BLAST is the one publication thoroughly dedicated to this renowned suite of instruments. It deals biologists, computational biology scholars, and bioinformatics execs a transparent realizing of BLAST in addition to the technology it helps. This ebook exhibits you the way to maneuver past the default parameters, get particular solutions utilizing BLAST, and the way to interpret your effects. The booklet additionally comprises instructional and reference sections overlaying NCBI-BLAST and WU-BLAST, history fabric that can assist you comprehend the statistics at the back of BLAST, Perl scripts that can assist you arrange your information and research your effects, and a wealth of suggestions and tips for configuring BLAST to satisfy your individual study wishes.

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This formulation, known as Shannon's Entropy (named after Claude Shannon), is shown in Figure 4-2. Figure 4-2. Equation 4-2 Entropy (H) is the negative sum over all the symbols (n) of the probability of a symbol (pi) multiplied by the log base 2 of the probability of a symbol (log2pi). Let's work through a couple of examples to make this clear. 5 and therefore a log2 probability of -1. 5)(-1) ) = 1 bit Suppose you have a trick coin that comes up heads 3/4 of the time. Since you're a little more certain of the outcome, you expect the entropy to decrease.

The sequences that end up in the mature mRNA are called exons, and the intervening stuff is called introns. The part of the mRNA that codes for protein is called the coding sequence (CDS), and the parts at either end are called untranslated regions (UTRs). The other common post-transcriptional modification is poly-adenylation. In this process, 50 or more adenine nucleotides are added to the end of the mRNA, which is called a poly-A tail. Figure 2-6. 4 Biological Sequences and Similarity The beginning of this chapter asked why biological sequences are similar to one another.

People are sometimes surprised to find that genome size and chromosome number aren't reflected in organismal complexity. For example, the single-celled Amoeba dubia has a genome that is about 200 times larger than the human genome. Although dogs and cats have very similar genome sizes, dogs have twice as many chromosomes. One rule to keep in mind when thinking about genomic organization is that genomes of viruses and prokaryotic organisms generally contain little noncoding sequence, whereas the genomes of more complex organisms usually contain a much higher percentage of noncoding sequence.

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