BIF601 HANDOUTS PDF | Bioinformatics Computing-I Notes


BIF601: Bioinformatics Computing I (PDF)

Bioinformatics is a multidisciplinary field that develops software and tools for understanding biological data, especially where data sets are large and complex. As a multidisciplinary science field, bioinformatics combines biology, chemistry, physics, computer science, information engineering, mathematics, and mathematics to analyze and interpret biological data. BIF601 HANDOUTS

Course Category: Bioinformatics

Course Outline

Database, Database Advantages, Data Management, Database Software, Computer Network, Data Communication, Data communication, Communication tasks and protocols, Topology, Topology and Transmission modes, Geographical Scope and Communication Models, Communication Models and transmission Technology, Communication Models and transmission Technology, Communication Models and transmission Technology, Bandwidth/Frequency Spectrum, Network Security, Information retrieval and Search engines, information retrieval introduction,

IRModels, Revaluation Measures, R in Biological DBs, IR in Bioinformatics, search engines, ML Evaluation, search engine categories, EMRs, EHRs, Knowledge discovery, knowledge discovery techniques, Bayes’ theorem, Decision Tree, neural networks, Association rule, clustering, Machine learning, Ml applications, ML Other Applications, Data integration, Problems with data integration, Pattern Finding, Brute Force Algorithm, KMP Algorithm, KMP Prefix function, KMP Matcher, Boyer Moore Algorithm, Dot Plots, Scoring Scheme, Substitution Matrices, Optimal Algos, Needleman_wunch Algos, Needleman_wunch Execution, Smith_waterman Algo, BIF601 HANDOUTS PDF

PSA Complex Models, Computer Programs,  Programming languages, Java Introduction, anatomy of Java Program, Introduction to Bio Java, Alphabets, Symbols and Sequences, Central Dogma, Sequence Input-Output, Features and Annotations, Protein structure modules, Alignment Module, Matlab introduction, Matlab Basics, BioInformatics Toolbox, features, and functions, bioinformatics tasks, Phylogenetic analysis, proteins and as, Introduction To Python, Python Basics, BioPython Basics, Introduction To BioPython, SequenceObject, Phylogenetic tree IO, PHP part-1, PHP part-2, PHP part-3, Perl Basics, BIF601 HANDOUTS PDF

Unix/Linux Commands, Shell Scripting, Multiple Sequence Alignment, More on Multiple Sequence Alignment, Progressive Alignment for MSA, MSA Example, CLUSTAL, Structure Visualization – I, Structure Visualization – II, Experimental Determination of Protein Structure, Protein Data Bank, Visualization Techniques, Online Resources for Protein Visualization, Types of Protein Visualizations


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BIF601: Bioinformatics Computing I Handouts

Biological sequences

Biological sequences are the product of evolutionary history and phylogenies are the epitome of that history. A simple and widely used model of evolution is a doubletree. As described earlier (Section 3.4), the tree contains nodes and edges that connect the nodes. The leaves on the phylogenetic tree represent the existing sequences of living organisms.

Optimal Pairwise Alignment

Organisms are the result of evolutionary history. This has important implications for biological function, whether physical or cellular. In classical biology, organs derived from a common ancestor are called homologous. For example, the human hand is like a baboon’s hand, a cat’s paw, and a bat’s wing. These structures are characterized by common anatomical features and similar functions, albeit very different. In contrast, the wings of bats and flies are not the same and are very different in shape, although they are both flight organs. Such organs are said to be identical. To put things simply, homology often suggests similarities in work, whereas similarities in workmanship may be due to similarities or homology.

  Scoring Alignment

A small alignment unit contains one location from each of the two comparable sequences. When hitting such a pair of positions it is customary to distinguish between pairs that include two remains and pairs that form part of an indel. In the case of indels, the simplest method of modeling is known as the line gap model. In cellular biology to search for similar traits, in this case, DNA residues or protein sequences reappear through a description of the alignment problem. As explained in detail below, the two sequences are aligned by writing homologous fossils on top of each other. This may or may not work well, i.e. the resulting alignment may be satisfactory or unsatisfactory.

When two proteins are compatible, they are often identical. Moreover, they often have the same tasks. The fact that the same sequence includes the same functions is the reason why we start this book with algorithms aligned: such algorithms are used to find the same known sequence. Work and thus successfully determined on the initial assumption of the genetic function of the novel.

 Amino Acid Substitution Matrices        

Today, there is far more nucleotide than protein sequence data available. This reflects the fact that the genomes are larger than the proteome they make. However, the protein sequence began before the discovery of a double-helical structure. DNA in 1953. Between 1949 and 1955 the first complete sequence of proteins, that of bovine insulin, was determined by Fred Sanger and colleagues [129, p. 212]. It was only once that Sanger and Maxam and Gilbert independently developed simple DNA sequencing methods in the mid-1970s when the nucleotide genotype of an organism became more accessible than its protein phenotype.

For early development alignment proteins algorithms were therefore focused on research. Molecular biologists often refer to “the sequence of proteins”. This is a summary to say that the sequence of the protein code has changed. Due to the breakdown of genetic code, the conversion rate between amino acids varies from one to three steps.


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BIF601: Bioinformatics Computing I Handouts (pdf)