<![CDATA[BOL: Bioinformatics Algorithm Demonstrations and Tutorials]]> https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials?annoff=25 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials Thu, 29 Aug 2013 09:23:51 -0500 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials <![CDATA[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 ". 

Address of the bookmark: http://www.cybertory.org/downloads/bae/BioinformaticsAlgorithmsExcelDoc.pdf

]]> Jitendra Narayan https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-954 Sat, 16 Nov 2013 23:15:59 -0600 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-954 <![CDATA[Comment by Manisha Mishra]]> 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

]]> Manisha Mishra https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-953 Fri, 15 Nov 2013 15:27:35 -0600 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-953 <![CDATA[Comment by Rahul Nayak]]> Original paper of Basic local alignment search tool algorithms http://www.cmu.edu/bio/education/courses/03510/LectureNotes/Altschul1990.pdf

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-950 Fri, 15 Nov 2013 04:53:31 -0600 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-950 <![CDATA[Comment by Shikha Logwani]]> 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

]]> Shikha Logwani https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-942 Thu, 14 Nov 2013 21:20:21 -0600 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-942 <![CDATA[Comment by Poonam Mahapatra]]> A Fast Recursive Algorithm for Optimum Sequential Signal Detection in a BLAST System http://externe.emt.inrs.ca/users/benesty/papers/sp_jul2003.pdf

]]> Poonam Mahapatra https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-913 Tue, 12 Nov 2013 06:55:51 -0600 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-913 <![CDATA[Comment by Surajeet]]> 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

]]> Surajeet https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-909 Sun, 10 Nov 2013 21:48:54 -0600 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-909 <![CDATA[Comment by Kamalakshi Mukherjee]]> Applications of genetic algorithms in bioinformatics http://scholarworks.sjsu.edu/cgi/viewcontent.cgi?article=4491&context=etd_theses

]]> Kamalakshi Mukherjee https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-906 Sun, 10 Nov 2013 11:06:55 -0600 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-906 <![CDATA[Comment by Rahul Nayak]]> Locality and Parallelism Optimization for Dynamic Programming Algorithm in Bioinformatics http://www.bioperf.org/TSF06.pdf

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-905 Sun, 10 Nov 2013 08:01:04 -0600 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-905 <![CDATA[Comment by Mukesh Jha]]> Pattern Recognition Algorithms

http://www.eui.upm.es/~fmartin/webpgomez/Docencia/Pattern-Recognition/

]]> Mukesh Jha https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-904 Sun, 10 Nov 2013 07:55:39 -0600 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-904 <![CDATA[Comment by Mukesh Jha]]> A SURVEY OF SEQUENCE MATCHING AND ALIGNMENT ALGORITHMS https://people.ok.ubc.ca/rlawrenc/teaching/404/Project/Samples/Report/SequenceMatching_Report.pdf

]]> Mukesh Jha https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-898 Sat, 09 Nov 2013 18:05:25 -0600 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-898 <![CDATA[Comment by Surabhi Chaudhary]]> One of my favourite lecture notes on "String Matching Problems and Bioinformatics" http://users.csc.calpoly.edu/~dekhtyar/448-Spring2013/lectures/lec03.448.pdf

]]> Surabhi Chaudhary https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-897 Sat, 09 Nov 2013 17:58:31 -0600 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-897 <![CDATA[Comment by Surabhi Chaudhary]]> Fast Dynamic Algorithm for Sequence Alignment based on Bioinformatics http://research.ijcaonline.org/volume37/number7/pxc3876636.pdf

]]> Surabhi Chaudhary https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-893 Fri, 08 Nov 2013 07:52:59 -0600 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-893 <![CDATA[Comment by Rahul Nayak]]> Hidden Markov Models in Bioinformatics http://www.benthamscience.com/cbio/Samples/cbio2-1/0005CBIO.pdf

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-892 Fri, 08 Nov 2013 06:05:07 -0600 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-892 <![CDATA[Comment by Aadesh Goswami]]> 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/

]]> Aadesh Goswami https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-889 Thu, 07 Nov 2013 18:28:33 -0600 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-889 <![CDATA[Comment by Manisha Mishra]]> An excellent bioinformatics algorithms notes, and descriptive tutorial http://www.vaughaneveleigh.co.uk/wp-content/uploads/2012/02/Bioinformatics-Algorithms.pdf

]]> Manisha Mishra https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-888 Thu, 07 Nov 2013 18:24:29 -0600 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-888 <![CDATA[Comment by Manisha Mishra]]> 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/

]]> Manisha Mishra https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-886 Thu, 07 Nov 2013 18:11:59 -0600 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-886 <![CDATA[Comment by Mukesh Jha]]> 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

]]> Mukesh Jha https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-885 Thu, 07 Nov 2013 18:09:14 -0600 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-885 <![CDATA[Comment by Mukesh Jha]]> Introduction to algorithms in bioinformatics by István Miklós http://www.renyi.hu/~miklosi/AlgorithmsOfBioinformatics.pdf

]]> Mukesh Jha https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-881 Wed, 06 Nov 2013 05:52:07 -0600 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-881 <![CDATA[Comment by Surajeet]]> Applications of artificial intelligence in bioinformatics: A review by Zoheir http://www.csis.pace.edu/~ctappert/dps/d861-07/team2-AI.pdf

]]> Surajeet https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-843 Mon, 21 Oct 2013 10:03:07 -0500 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-843 <![CDATA[Comment by Shikha Logwani]]> Algorithms pseudocodes http://aima.cs.berkeley.edu/algorithms.pdf

]]> Shikha Logwani https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-778 Thu, 26 Sep 2013 12:34:49 -0500 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-778 <![CDATA[Comment by Rahul Nayak]]> I found a really good resource for Artificial Intelligence in Bioinformatics @ http://www.aisb.org.uk/publications/proceedings/aisb2000/AISB00_Bioinformatics.pdf

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-776 Thu, 26 Sep 2013 11:18:16 -0500 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-776 <![CDATA[Comment by Rahul Nayak]]> 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

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-713 Mon, 09 Sep 2013 06:35:14 -0500 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-713 <![CDATA[Comment by Radha Agarkar]]> Tree Edit Distance Problems: Algorithms and Applications to Bioinformatics @ http://repository.kulib.kyoto-u.ac.jp/dspace/bitstream/2433/139423/1/transinf.E93.D.208.pdf]]> Radha Agarkar https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-683 Wed, 04 Sep 2013 09:03:15 -0500 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-683 <![CDATA[Comment by Kamalakshi Mukherjee]]> Bioinformatics and Sequence Alignment tutorial by University of Illinois at Urbana-Champaign, Luthey-Schulten Group

http://www.ks.uiuc.edu/Training/Tutorials/science/bioinformatics-tutorial/bioinformatics.pdf

]]> Kamalakshi Mukherjee https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-682 Wed, 04 Sep 2013 08:45:00 -0500 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-682 <![CDATA[Comment by Kamalakshi Mukherjee]]> Main Algorithms with Applications in Bioinformatics http://www.math-info.univ-paris5.fr/~nuel/lecture_main_algo.pdf]]> Kamalakshi Mukherjee https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-607 Sat, 31 Aug 2013 10:06:15 -0500 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-607 <![CDATA[Comment by Jitendra Narayan]]> Machine Learning in Bioinformatics: Algorithms,Implementations & Applications thesis by Robert http://proteomics.bioengr.uic.edu/people/ezra/cv/thesis_uic.pdf

]]> Jitendra Narayan