Essential Bioinformatics and Biocomputing (LSM2104: Section I) Biological Databases and Bioinformatics Software Prof. Chen Yu Zong Tel: Room 07-24, level 7, SOC1, NUS January

Essential Bioinformatics and Biocomputing (LSM2104)2 Lecture 5: Bioinformatics software Outline: –Types of bioinformatics software Sequence, pattern and domain Evolutionary analysis Visualization Modeling and prediction (sequence, structure and function) Data mining (bibliographic and text searches) –Examples

Essential Bioinformatics and Biocomputing (LSM2104)3 Types of Bioinformatics software 1.Analysis of biological data/systems and characterization of molecules and sequences. 2.Analysis and interpretation of experimental results 3.Simulation of laboratory experiments, important for tackling large scale problems 4.Predictions that lead to the design of experiments 5.Bioinformatics software can be accessed via WWW, or through integrated software packages (such as Emboss, GCG, Staden, DNAstar, …). It may be coupled with databases, or may stand alone.

Essential Bioinformatics and Biocomputing (LSM2104)4 Bioinformatics software Major sources Software package at ExPASy Molecular Biology Server ; Software at PBIL Bio-Informatique Lyonnais Toolbox at EBI European Bioinformatics Institute

Essential Bioinformatics and Biocomputing (LSM2104)5 Bioinformatics software Major types of bioinformatics tools Sequence analysis tools Sequence comparison Pattern and domain search Evolutionary analysis Prediction of sequence structure and function Visualization of molecular structures Structure modeling Bibliographic and text searches Specialized and other tools

Essential Bioinformatics and Biocomputing (LSM2104)6 Bioinformatics software Sequence analysis tools This kind of software focuses on extraction and comparison of properties in DNA and protein sequences –Sequence analysis provides for identification of domains, structure, and function, and other properties -The analysis of individual sequences helps with sequence comparison Textbook chapter 5, pages 81-93

Essential Bioinformatics and Biocomputing (LSM2104)7 Bioinformatics software Sequence analysis tools This kind of software focuses on extraction and comparison of DNA and protein sequence properties such as –composition of nucleotide or protein sequences –codon usage in DNA –translation and backtranslation Textbook chapter 5, pages 81-93

Essential Bioinformatics and Biocomputing (LSM2104)8 Bioinformatics software Composition of nucleotide or protein sequences Composition (frequency of occurrence of a nucleotide or of an amino acid) is the most basic analysis. It can give us important functional and structural clues. For example, CG-rich regions called CpG islands are often found in promoters. A short region just before the splice site at the end of introns often has high C+T content.

Essential Bioinformatics and Biocomputing (LSM2104)9 Bioinformatics software Composition of protein and DNA sequences Web: Network Protein (Amino-acid composition) –AA Composition JEMBOSS (in our own laboratory) – (nucleic, composition, compseq)

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Essential Bioinformatics and Biocomputing (LSM2104)12 Bioinformatics software Codon usage in DNA Web: –Count-codon program in Codon Usage Database (needs start and stop codons at the start and the end of the sequence) –Tool for Gene to Codon Usage Table –(does not care about start and stop codons) JEMBOSS (in the laboratory) – (nucleic, codon usage, cusp) DNA coding region should have only one stop codon

Essential Bioinformatics and Biocomputing (LSM2104)13 Bioinformatics software

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Essential Bioinformatics and Biocomputing (LSM2104)15 Bioinformatics software Translation (DNA to protein) and back translation (protein to DNA) Web: –Translate tool at ExPASy (DNA to protein) JEMBOSS (in the laboratory) – (DNA to protein and reverse) (nucleic, translation, transeq; nucleic, translation, backtranseq) If we translate and back translate the same sequence we will typically not get the same sequence as the starting one.

Essential Bioinformatics and Biocomputing (LSM2104)16 Bioinformatics Software Sequence comparison (the most important software) This will be taught next month by A/P Tan Tin Wee. Web: Local alignment (BLAST, FASTA) – – – Multiple alignment (Clustal W) – JEMBOSS (in the laboratory) – Local alignment: Smith-Waterman (alignment, local, water) Global alignment: Needleman-Wunsh (alignment, global, needle)

Essential Bioinformatics and Biocomputing (LSM2104)17 Bioinformatics software Evolutionary analysis Multiple sequence alignments can be used as measures of evolutionary distance between proteins. The phylogeny systems are used to represent evolutionary distances between sequences. WebPhylip GeneBee Read textbook, page 83.

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Essential Bioinformatics and Biocomputing (LSM2104)19 Bioinformatics software Prediction of sequence structure and function Sequences that have similar structure often have similar function. For many sequences we can extract secondary and tertiary structure from the PDB database. What if our sequence is not in the PDB? We can predict structure of a biological sequence using appropriate software. There are several programs for prediction of secondary structure. For prediction of tertiary structure we can do modelling. (PHD method for secondary structure prediction)

Essential Bioinformatics and Biocomputing (LSM2104)20 Bioinformatics software Secondary structure prediction:

Essential Bioinformatics and Biocomputing (LSM2104)21 Bioinformatics software Secondary structure prediction: –The PHD program predicted four alpha helices in the human IL-2 (red). The number of helices is correct, but their lengths and boundaries are not correct (purple). –When we make a prediction in bioinformatics, we must have an idea about the accuracy of prediction programs. –To assess the accuracy of a program, we can test it with known data. Our test must have sufficient examples, so that we can make reasonable conclusions.

Essential Bioinformatics and Biocomputing (LSM2104)22 Secondary structure prediction Bioinformatics software alpha –Lactalbumin PDB 1A4V

Essential Bioinformatics and Biocomputing (LSM2104)23 Bioinformatics software We used nine different programs for prediction of secondary structure of alpha–Lactalbumin (PDB 1A4V). The results show that the best predictions for this molecule were from “Predator”, while DSC was the laggard. This test does not mean that Predator is the best of the tested programs, nor that DSC is the worst. To make such conclusions we must make test set first. The test set should contain the examples from the family of proteins that our query protein belongs to. The learning point – none of the prediction programs (and this applies across all bioinformatics software, not only secondary structure prediction) is 100% accurate. The users must be cautious when interpreting results from the predictive software.

Essential Bioinformatics and Biocomputing (LSM2104)24 Bioinformatics software Common measure (other measures also exist) Sensitivity SE=TP/(TP+FN) Specificity SP=TN/(TN+FP) For example, prediction of binding peptides to a particular receptor Experimental Predicted Class Example 1 Binder Binder True positive (TP) Example 2 Non-binder Non-binder True negative (TN) Example 3 Binder Non-binder False negative (FN) Example 4 Non-binder Binder False positive (FP) Prediction system that has SE=0.8 and SP=0.9 will correctly predict 8 of 10 experimental positives, and for each 10 experimental negatives it will make one false prediction. This prediction accuracy may be very good for prediction of peptide binding, but is not very good for some other predictions, for example gene prediction.

Essential Bioinformatics and Biocomputing (LSM2104)25 Bioinformatics software Prediction of 3-D structure Various modelling programs –comparative modelling, using known structures as templates –ab initio modelling, using atomic simulation, residue statistics, etc. These methods will be covered later in the course An example of the comparative modelling software is SWISS- MODEL This model is provided by . This tool has the facility for assessing the quality of predictions

Essential Bioinformatics and Biocomputing (LSM2104)26 Bioinformatics software

Essential Bioinformatics and Biocomputing (LSM2104)27 Bioinformatics software

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Essential Bioinformatics and Biocomputing (LSM2104)29 Bioinformatics software Software for visualisation of 3-D structures. Provides different views to 3-D molecular structure, which will be taught by A/P Shoba. –Chime, Rasmol (they use files in PDB format) –Scorpion database uses Chime. Chime can be downloaded from:

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Essential Bioinformatics and Biocomputing (LSM2104)32 Bioinformatics software Text searches Text searching software is used associated with databases. Most commonly we search by keywords or combinations of keywords. Examples of PubMed searches: –Diabetes –181,672 matches –Diabetes AND IDDM – 35,841 –Diabetes AND IDDM AND autoimmunity – 1,109 –Diabetes OR autoimmunity – 190,674 –Diabetes[Title/Abstract] – 114,624 The last example is more advanced PubMed option “preview/index”

Essential Bioinformatics and Biocomputing (LSM2104)33 Summary of Today’s lecture Bioinformatics software Summary of Today’s lecture Why bioinformatics software? Types of software: sequence, motif, evolution, visualization, structural modeling, simulation, test search. Examples of selected software: –Sequence composition –DNA-protein sequence translation –Evolutionary analysis –Protein secondary structure prediction –Comparative modeling –Text search To be taught later: Sequence comparison, visualization etc.

Essential Bioinformatics and Biocomputing (LSM2104)34 Summary of the Section: Biological databases and bioinformatics software We first focused on biological databases. We covered topics: –discussed types of biological databases –briefly described popular databases –structure of the GenBank and SWISS-PROT entries –searching biological databases –types of questions that can be answered by searching databases –completeness and errors in the databases

Essential Bioinformatics and Biocomputing (LSM2104)35 Summary of the Section: Biological databases and bioinformatics software The second topic was bioinformatics software. We covered: –why do we need bioinformatics software? –briefly described major types of bioinformatics software –described software for sequence composition, codon usage, translation and backtranslation –introduced the concept of sequence alignment, evolutionary analysis –secondary and tertiary structure prediction, molecular visualization –accuracy of prediction software –text searching