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
A graph-theory algorithm for rapid protein side-chain prediction.
More @ http://www.ncbi.nlm.nih.gov/pubmed/12930999
Bioinformatics Algorithms; Techniques and Application book provide an in-depth survey of the most important developments in bioinformatics algorithms in the postgenomic era.
More @ http://urania.udea.edu.co/sitios/astronomia-2.0/pages/descargas.rs/files/descargasdt5vi/Cursos/CursosEspeciales/HerramientasComputacionales/2011-2/Referencias/Mandoi_et_al2008-BioinformaticsAlgorithms.pdf
http://webdocs.cs.ualberta.ca/~ys3/Publications/scl08.pdf
Introduction to Bioinformatics Algorithms tutorial provide a good overview of algorithms http://www.cse.sc.edu/~maxal/csce590b/Lect01-02.pdf
Introduction to Bioinformatics Algorithms by Jones and Pevzner http://read.pudn.com/downloads160/ebook/722845/Intro%20to%20Bioinformatics%20Algorithms.pdf
There are lots of books on bioinformatics algorithms, but I personally found this online book "Introduction to algorithms in bioinformatics" very easy to follow and understand.
Note1: http://www.renyi.hu/~miklosi/AlgorithmsOfBioinformatics.pdf
Note2: http://www.vaughaneveleigh.co.uk/wp-content/uploads/2012/02/Bioinformatics-Algorithms.pdf
Global sequence alignment using Needleman/Wunsch techniques ... Dynamic Programming http://www.avatar.se/molbioinfo2001/dynprog/dynamic.html
Applications of genetic algorithms in bioinformatics by Amie @ http://scholarworks.sjsu.edu/cgi/viewcontent.cgi?article=4491&context=etd_theses
Bioinformatics and Sequence Alignment http://www.ks.uiuc.edu/Training/Tutorials/science/bioinformatics-tutorial/bioinformatics.pdf
Support Vector Machines in Bioinformatics: a Survey
http://home.deib.polimi.it/chicco/SVM_in_Bioinformatics-TR_-_DavideChicco_2012-10-12.pdf
Heuristic Algorithms in Bioinformatics http://users-birc.au.dk/cstorm/students/Vesterstroem_Mar2006.pdf
Machine Learning in Bioinformatics: Algorithms,Implementations & Applications thesis by Robert http://proteomics.bioengr.uic.edu/people/ezra/cv/thesis_uic.pdf
http://www.ks.uiuc.edu/Training/Tutorials/science/bioinformatics-tutorial/bioinformatics.pdf
I found some good resources from AI articles, specifically from McGill University's COMP-644 (Pattern Recognition) course.
http://cgm.cs.mcgill.ca/~godfried/teaching/pr-web.html
I found a really good resource for Artificial Intelligence in Bioinformatics @ http://www.aisb.org.uk/publications/proceedings/aisb2000/AISB00_Bioinformatics.pdf
Algorithms pseudocodes http://aima.cs.berkeley.edu/algorithms.pdf
Applications of artificial intelligence in bioinformatics: A review by Zoheir http://www.csis.pace.edu/~ctappert/dps/d861-07/team2-AI.pdf
Introduction to algorithms in bioinformatics by István Miklós http://www.renyi.hu/~miklosi/AlgorithmsOfBioinformatics.pdf
BIOINFORMATICS ALGORITHMS, Techniques and Applications book suits to newbie bioinformatician http://urania.udea.edu.co/sitios/astronomia-2.0/pages/descargas.rs/files/descargasdt5vi/Cursos/CursosEspeciales/HerramientasComputacionales/2011-2/Referencias/Mandoi_et_al2008-BioinformaticsAlgorithms.pdf
Machine Learning Approaches to Bioinformatics http://www.asianscientist.com/books/wp-content/uploads/2013/06/7454_chap01.pdf
Other chapters of this book at
http://www.asianscientist.com/books/wp-content/uploads/2013/06/
An excellent bioinformatics algorithms notes, and descriptive tutorial http://www.vaughaneveleigh.co.uk/wp-content/uploads/2012/02/Bioinformatics-Algorithms.pdf
Impact of Parallel Computing on Bioinformatics Algorithms are well documented in this paper http://icacct.apiit.edu.in/download/all%20chapters/CHAPTER-44.pdf
Other useful links:
http://icacct.apiit.edu.in/download/all%20chapters/
Hidden Markov Models in Bioinformatics http://www.benthamscience.com/cbio/Samples/cbio2-1/0005CBIO.pdf
Fast Dynamic Algorithm for Sequence Alignment based on Bioinformatics http://research.ijcaonline.org/volume37/number7/pxc3876636.pdf