Bioinformatics Algorithms
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Bioinformatics Algorithm Demonstrations and Tutorials
Abstract
This project presents demonstrations of selected computer science algorithms important in bioinformatics, implemented in the spreadsheet program Microsoft Excel. Spreadsheets provide an interesting platform for demonstration of algorithms, since various steps of the calculations can be exposed in a manner that is easily comprehensible to users with little programming experience. The algorithms demonstrated include two approaches to approximate string matching (dynamic programming and Shift-AND numeric approximate matching), Hierarchical Clustering (used in phylogenetic studies and microarray analysis of gene expression), a Naive Bayes Classifier for simulated microarray gene expression data, and a simple Neural Network. These demonstrations are designed to serve as instructional aids in bioinformatics courses.
Tutorial @ http://www.cybertory.org/downloads/bae/BioinformaticsAlgorithmsInExcel.zip
One of the best resource for online bioinformatics learning is https://stepic.org/Bioinformatics-Algorithms-2 Enjoy the online learning.
Reference : cybertory
" Please add your favourite bioinformatics algorithms and tutorial links below in the comment section, for the benefit of bioinformatics and computational biology community ".
Comments
One of my favourite lecture notes on "String Matching Problems and Bioinformatics" http://users.csc.calpoly.edu/~dekhtyar/448-Spring2013/lectures/lec03.448.pdf
A SURVEY OF SEQUENCE MATCHING AND ALIGNMENT ALGORITHMS https://people.ok.ubc.ca/rlawrenc/teaching/404/Project/Samples/Report/SequenceMatching_Report.pdf
Pattern Recognition Algorithms
http://www.eui.upm.es/~fmartin/webpgomez/Docencia/Pattern-Recognition/
Locality and Parallelism Optimization for Dynamic Programming Algorithm in Bioinformatics http://www.bioperf.org/TSF06.pdf
Applications of genetic algorithms in bioinformatics http://scholarworks.sjsu.edu/cgi/viewcontent.cgi?article=4491&context=etd_theses
Bioinformatics Algorithms: Dynamic Programming by David Hoksza http://siret.ms.mff.cuni.cz/hoksza/teaching/vscht/bioinfoalgo/2012/presentations/lecture02.pdf
Bioinformatics Algorithms Book @ http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.218.3258&rep=rep1&type=pdf
A Fast Recursive Algorithm for Optimum Sequential Signal Detection in a BLAST System http://externe.emt.inrs.ca/users/benesty/papers/sp_jul2003.pdf
Hidden Markov Models, Viterbi Algorithm, Markov Chain Exploration with source-codes http://bioinformaticsonline.com/pages/view/6380/hidden-markov-models-viterbi-algorithm-markov-chain-exploration-with-script
Original paper of Basic local alignment search tool algorithms http://www.cmu.edu/bio/education/courses/03510/LectureNotes/Altschul1990.pdf
Efficient Systems Biology Algorithms for Biological Networks over Multiple Time-Scales: From Evolutionary to Regulatory Time
http://cs.nyu.edu/mishra/PEOPLE/mitrofanova_antonina.pdf
Graph Theory and Networks in Biology by Oliver Mason and Mark Verwoerd http://www.hamilton.ie/systemsbiology/files/2006/graph_theory_and_networks_in_biology.pdf
A Quantum Algorithm for Closest Pattern Matching
http://sqig.math.ist.utl.pt/pub/MateusP/05-MO-quantlog05s.pdf
Biological Sequence Matching using Boolean algebra vs. Fuzzy Logic http://www.ijcaonline.org/volume26/number11/pxc3874383.pdf
Applications of artificial intelligence in bioinformatics : A review Zoheir Ezziane http://www.csis.pace.edu/~ctappert/dps/d861-07/team2-AI.pdf
Soft Computing Methodologies in Bioinformatics http://pdf.aminer.org/000/305/056/positive_and_negative_combination_effects_of_crossover_and_mutation_operators.pdf
Implementing Hidden Markov Models(HMM) for Information Extraction in Perl http://www.lwebzem.com/cgi-bin/res/HMM.html
Approximate Matching with Suffix Trees http://homepage.usask.ca/~ctl271/810/approximate_matching.shtml
Fuzzy Logic in Medicine and Bioinformatics http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1559939/
Using Fuzzy Logic to Solve Bioinformatics Tasks https://ortus.rtu.lv/science/lv/publications/8859/fulltext
HMM tutorial http://jedlik.phy.bme.hu/~gerjanos/HMM/node2.html
Application of graph theory algorithm for rapid protein side-chain prediction http://www.ncbi.nlm.nih.gov/pubmed/12930999
A lecture notes series by Can Alkan and Shatlyk Ashyralyev on Introduction to Bioinformatics Algorithms: A Computational Molecular Biology Approaches can be found at http://www.cs.bilkent.edu.tr/~calkan/teaching/cs481/
Bioinformatics algorithms in Java at http://neobio.sourceforge.net/
Machine learning in bioinformatics tutorial at http://proteomics.bioengr.uic.edu/people/ezra/cv/thesis_uic.pdf
Algorithms in Bioinformatics http://www.iis.sinica.edu.tw/~hil/bioinfo/