<![CDATA[BOL: Bioinformatics Algorithm Demonstrations and Tutorials]]> https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials? 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-1505 Tue, 24 Jun 2014 00:11:39 -0500 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1505 <![CDATA[Comment by John Parker]]> Useful algorithms bookmarked http://bioinformaticsonline.com/bookmarks/view/12206/bioinformatics-algorithms-tutorials

]]> John Parker https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1504 Tue, 24 Jun 2014 00:07:33 -0500 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1504 <![CDATA[Comment by John Parker]]> Useful bioinformatics algorithms tutorials http://homolog.us/wiki1/index.php?title=Main_Page

]]> John Parker https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1503 Tue, 24 Jun 2014 00:06:22 -0500 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1503 <![CDATA[Comment by John Parker]]> Burrows Wheeler transform in animation http://www.homolog.us/animation/

]]> John Parker https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1437 Thu, 29 May 2014 14:07:10 -0500 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1437 <![CDATA[Comment by Jit]]> A new trainable, high-speed and biologically relevant alignment algorithms of high-throughput sequencing reads to coding DNA http://nar.oxfordjournals.org/content/early/2014/05/26/nar.gku473.full

]]> Jit https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1413 Wed, 21 May 2014 15:44:23 -0500 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1413 <![CDATA[Comment by Alok Prajapati]]> The FindMotif.pl program uses position-specific scoring matrices to search for sequences similar to a consensus sequence. Find more at http://www.people.vcu.edu/~elhaij/IntroBioinf/Notes/PSSM-Perl.html

]]> Alok Prajapati https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1368 Sat, 10 May 2014 00:42:13 -0500 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1368 <![CDATA[Comment by Jitendra Narayan]]> Parallelized pairwise sequence alignment using CUDA on multiple GPUs http://www.biomedcentral.com/1471-2105/10/S7/A3

]]> Jitendra Narayan https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1347 Tue, 22 Apr 2014 12:06:39 -0500 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1347 <![CDATA[Comment by Jitendra Narayan]]> Bioinformatics algorithms coursera
https://github.com/jschendel/bioinformatics-algorithms-coursera

]]> Jitendra Narayan https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1343 Mon, 21 Apr 2014 21:44:09 -0500 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1343 <![CDATA[Comment by Alok Prajapati]]> MSA algorithms http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3261699/

]]> Alok Prajapati https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1336 Fri, 18 Apr 2014 03:30:15 -0500 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1336 <![CDATA[Comment by Jit]]> A library of efficient bioinformatics algorithms http://www.statistica.unimib.it/~dellavedova/papers/ALiBio-applied-bioinformatics.pdf

]]> Jit https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1335 Fri, 18 Apr 2014 03:28:43 -0500 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1335 <![CDATA[Comment by Rahul Nayak]]> Introduction to Genetic Algorithms http://lancet.mit.edu/mbwall/presentations/IntroToGAs/

http://l1apc2.ens.utulsa.edu/~rogerw/cs7623/GA-Tutorial-93.doc

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1334 Fri, 18 Apr 2014 03:25:56 -0500 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1334 <![CDATA[Comment by Rahul Nayak]]> Algorithms in Bioinformatics http://www.iis.sinica.edu.tw/~hil/bioinfo/

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1268 Sat, 15 Mar 2014 03:33:06 -0500 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1268 <![CDATA[Comment by Jit]]> Machine learning in bioinformatics tutorial at http://proteomics.bioengr.uic.edu/people/ezra/cv/thesis_uic.pdf

]]> Jit https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1265 Sat, 15 Mar 2014 03:26:20 -0500 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1265 <![CDATA[Comment by Jit]]> Bioinformatics algorithms in Java at http://neobio.sourceforge.net/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1236 Wed, 12 Mar 2014 10:42:04 -0500 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1236 <![CDATA[Comment by Prachi Taneja]]> 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/

]]> Prachi Taneja https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1235 Wed, 12 Mar 2014 10:39:02 -0500 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1235 <![CDATA[Comment by Prachi Taneja]]> Application of graph theory algorithm for rapid protein side-chain prediction http://www.ncbi.nlm.nih.gov/pubmed/12930999

]]> Prachi Taneja https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1205 Mon, 10 Mar 2014 03:29:55 -0500 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1205 <![CDATA[Comment by Rahul Nayak]]> HMM tutorial http://jedlik.phy.bme.hu/~gerjanos/HMM/node2.html

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1045 Thu, 19 Dec 2013 20:48:35 -0600 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1045 <![CDATA[Comment by Agampreet Kaur]]> Using Fuzzy Logic to Solve Bioinformatics Tasks https://ortus.rtu.lv/science/lv/publications/8859/fulltext

]]> Agampreet Kaur https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1044 Thu, 19 Dec 2013 20:47:55 -0600 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1044 <![CDATA[Comment by Agampreet Kaur]]> Fuzzy Logic in Medicine and Bioinformatics http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1559939/

]]> Agampreet Kaur https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1027 Tue, 03 Dec 2013 02:01:38 -0600 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-1027 <![CDATA[Comment by Rahul Nayak]]> Approximate Matching with Suffix Trees http://homepage.usask.ca/~ctl271/810/approximate_matching.shtml

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-987 Fri, 22 Nov 2013 13:49:23 -0600 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-987 <![CDATA[Comment by Aaryan Lokwani]]> Implementing Hidden Markov Models(HMM) for Information Extraction in Perl http://www.lwebzem.com/cgi-bin/res/HMM.html

]]> Aaryan Lokwani https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-965 Tue, 19 Nov 2013 09:31:21 -0600 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-965 <![CDATA[Comment by Surajeet]]> Soft Computing Methodologies in Bioinformatics http://pdf.aminer.org/000/305/056/positive_and_negative_combination_effects_of_crossover_and_mutation_operators.pdf

]]> Surajeet https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-964 Tue, 19 Nov 2013 09:25:07 -0600 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-964 <![CDATA[Comment by Rahul Nayak]]> Applications of artiļ¬cial intelligence in bioinformatics : A review Zoheir Ezziane http://www.csis.pace.edu/~ctappert/dps/d861-07/team2-AI.pdf

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-963 Tue, 19 Nov 2013 09:18:19 -0600 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-963 <![CDATA[Comment by Rahul Nayak]]> Biological Sequence Matching using Boolean algebra vs. Fuzzy Logic http://www.ijcaonline.org/volume26/number11/pxc3874383.pdf

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-958 Mon, 18 Nov 2013 18:00:28 -0600 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-958 <![CDATA[Comment by Rahul Nayak]]> A Quantum Algorithm for Closest Pattern Matching

http://sqig.math.ist.utl.pt/pub/MateusP/05-MO-quantlog05s.pdf

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-955 Sat, 16 Nov 2013 23:17:31 -0600 https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials#item-annotation-955 <![CDATA[Comment by Manisha Mishra]]> 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

]]> Manisha Mishra