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Topics in Teaching web:
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Changed: now 16:02 GMT
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Changed by:
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WebStatistics
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21 Aug 2008 - 08:23 - r1.161
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TWikiGuest
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// Statistics for Web // Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and uploads: // // Aug 2008 13037 10 0 883 431 WebStatistics 303 296 BioE131 259 215 CompbioTeaching 171 162 TWikiUsers 156 152 WebIndex 151 WebNotify 8 Main.IanHolmes 2 Main.TWikiGuest // Jul 2008 13078 20 0 734 498 BioE131 467 453 WebChanges 452 265 WebSearch 252 206 LizXiaSecondaryStructurePairwiseAlignmentGraduateProject 196 180 ...
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RNAFolding
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18 Aug 2008 - 12:14 - r1.3
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IanHolmes
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// RNA folding lab // In this lab you will learn to use the Main.VIENNA package and various related tools for analyzing, predicting the secondary structure of visualizing RNA sequences. // Fold a hammerhead ribozyme sequence // Data: // Rfam:RF00163 // Wikipedia:Hammerhead ribozyme // Genbank:AF404053.1 // Outline: // Read the RNAfold manual page // Fold a sequence with RNAfold //
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BioE131
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18 Aug 2008 - 11:00 - r1.255
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IanHolmes
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// BioE131/231 // Introduction to Computational Biology. // Course info // Code: Bioe131/231 // Title: Introduction to computational biology // Instructor: Ian Holmes (office hours: 11am-noon Wednesdays, 374C Stanley Hall; or by appointment) // GSI: Allison Berke (office hours: ... ) // When: //
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WebPreferences
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15 Aug 2008 - 12:37 - r1.21
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IanHolmes
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// Web Preferences // The following settings are web preferences of the web. These preferences overwrite the site-level preferences in ., and can be overwritten by user preferences (your personal topic, eg: .TWikiGuest in the web). // Preferences: // Top buttons // Set TOPBUTTONS // Koala skin: // Set SKIN koala // Set NAVBARH // Set NAVBARF // Set NOWEBSBAR //
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BioE131GSIFAQ
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31 Jul 2008 - 12:23 - r1.10
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IanHolmes
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// BioE131 GSI FAQ // What does the GSI do? // Before semester begins: // Meet with instructor // Look through lecture notes wiki // Clean up wiki (e.g. de-link solutions from previous year's labs homeworks) // Throughout semester (regular): // Prepare model answers to labs, homeworks, exams // Grade homeworks // Run labs // Hold office hours // Wiki gardening (e.g. lab pages, this FAQ, main page, etc.) //
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WebHome
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31 Jul 2008 - 11:58 - r1.39
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IanHolmes
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// Teaching links // Links on this page refer mostly to classes taught by Ian Holmes in the Department of Bioengineering at UC Berkeley. // Classes // Please select one of the following links: // Class wikis: // class wiki // Computational Biology class pages (more info): // Teaching.BioE131 //
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ChristopherVanBelleGraduateProject
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10 Jun 2008 - 14:33 - r1.34
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IanHolmes
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// Locating Classes of Functional Residues in a Protein via Estimation of Substitution Rates // Report // Here is the final report (183k PDF): // vanbelle bioe290b final.pdf // Overview // The Evolutionary Trace (ET) Method has been applied to protein families to predict functional determinants of proteins based upon their sequence similarity to other proteins in its family. ET identifies functional residues that are conserved within subfamilies and are responsible ...
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PathwayMining
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16 Dec 2007 - 22:54 - r1.41
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TWikiGuest
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// NOTE this lab is not currently working. Someone needs to go through this and make sure the right databases with the right types of accessions/names are set up. There's currently a disconnect somewhere. // Pathway Mining // Before we begin // The solution to hw6 is now posted: hw6a and hw6b. // Tools // This practical involves using getuniprot.pl, // a script that extracts, in FASTA format, the subset of Main.UniProt that // 1 has one or more annotations ...
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BioE241
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10 Dec 2007 - 10:00 - r1.160
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IanHolmes
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// BioE241 // Class info // Title: Probabilistic modeling in computational biology // Instructor: Main.IanHolmes // Class: !BioE 241 // When: Fall semester // Lectures: MF 11-12:30, 621 Stanley Hall // Note room change (previously 425 Hearst Mining Building) //
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Hw8Solution
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05 Dec 2007 - 20:01 - NEW
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JoshKittleson
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// # Program to simulate diffusion limited aggregation // # Given a grid size and an output file name, this program will // # seed the center of the grid with a particle, and then randomly // # release particles from the perimeter. Each particle performs // # a random walk through the grid, until it bumps into another // # particle, at which point it sticks. The simulation ends // # when a particle sticks on the edge of the grid. The grid // # is then output ...
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Hw7NoTreeNonUltrameric
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05 Dec 2007 - 19:40 - NEW
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JoshKittleson
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// #Implement UPGMA Treeless version Non-Ultrameric // ######Read in the distance matrix##### // # Get user input // $filename $ARGV 0 ; // # Validate input // if(!($filename)) // { // print "You must provide a filename!\n" ; // exit 1; // } // die "File $filename not found!\n" unless e $filename; //
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Hw7NoTreeUltrameric
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05 Dec 2007 - 19:40 - NEW
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JoshKittleson
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// # Implement UPGMA Treeless version Ultrameric // # Get user input // $filename $ARGV 0 ; // # Validate input // if(!($filename)) // { // print "You must provide a filename!\n" ; // exit 1; // } // # Read in the matrix //
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Hw7TreeUltrameric
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05 Dec 2007 - 19:39 - NEW
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JoshKittleson
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// #Implement UPGMA Tree Version Ultrameric // # Get user input // $filename $ARGV 0 ; // # Validate input // if(!($filename)) // { // print "You must provide a filename!\n" ; // exit 1; // } // # Read in the matrix //
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HolmesLabGraduateProjects
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04 Dec 2007 - 18:49 - r1.17
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IanHolmes
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// (This page is pretty out of date now... for an overview of research projects, contact IanHolmes.) // Holmes lab projects are annotated as follows: // Unix some Unix and scripting experience recommended // bio biological intuition helpful // coding programming experience would be good (e.g. C++) // math I classify these as mathematical // physics stochastic biophysics simulations // See lecture notes on Hidden Markov models for brief intro to xgram , ...
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DiffusionLimitedAggregation
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03 Dec 2007 - 21:03 - r1.33
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TWikiGuest
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// Diffusion-limited aggregation homework Due on Friday November 30th by 3:10. // This homework assignment is a little different from the bioinformatics-oriented exercises that we've done previously. // It involves simulating a random process of growth, that is similar to some models of the growth of bacterial colonies, but also turns up in physics (materials, crystals and other areas). // The purpose of the assignment is to simulate (with Perl) this basic ...
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FiniteStateMachines
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21 Nov 2007 - 14:25 - r1.9
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IanHolmes
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// Finite-state machines for sequence analysis // Pattern-matching // MCB binding site // digraph G { // START shape octagon, color black ; // END shape octagon, color black ; // L shape square, label "(any base)" ; // R shape square, label "(any base)" ; //
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ProtVizLab
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20 Nov 2007 - 21:52 - r1.74
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JoshKittleson
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// Protein Visualization Lab // // // Purpose // To find and visualize functional residues using ET and DARV, two different methods for amino acid conservation detection. // By the end of this lab... // By the end of this lab, you should be able to: //
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PrimatePhylogeny
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20 Nov 2007 - 10:37 - r1.102
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TWikiGuest
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// Primate phylogeny practical // Before we begin // The perl part of the solution to hw5 is posted here. Written portion here. // Goals // Investigate whether humans are, indeed, related to apes // Brief exposure to phylogenetic tree-building software // Procedure //
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ObjectUse
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18 Nov 2007 - 20:48 - r1.6
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JoshKittleson
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// Perl Objects and Modules The Uber-Short Users Guide // Modules // When you want to use someone else's code in perl, you use what are called perl modules. Refer back to slides 129+ from the lectures for a refresher, or see the Wikipedia page on the topic. Briefly, after the module has been installed (the GD module has been installed for you on the Etcheverry 1171 machines), you can just use code from that module in your own via the use statement. For example ...
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ImageConventions
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18 Nov 2007 - 19:57 - r1.2
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JoshKittleson
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// Images in Code: The Basics // An image, as displayed on your monitor, is a 2 dimensional array of pixels, where each pixel has a particular color. When working with an image inside of a program, that is exactly how to think about the image. There is one small oddity here: the upper left pixel is at index (0,0). As you increase x, you proceed to the right along the image, as you'd expect (32,0) is the 33rd pixel along the top row. However, as you increase ...
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RGBColors
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18 Nov 2007 - 19:26 - NEW
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JoshKittleson
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// white 255 255 255 // red 255 0 0 // green 0 255 0 // blue 0 0 255 // magenta 255 0 255 // cyan 0 255 255 // yellow 255 255 0 // black 0 0 0 // aquamarine 112 219 147 // blueviolet 159 95 159 // brass 181 166 66 // brightgold 217 217 25 // brown 166 42 42 //
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HW6b_solution
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18 Nov 2007 - 15:43 - NEW
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JoshKittleson
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// # This program examines three input files, E1, E2, and E3, where E1 contains a sample recording // # of the firing of a resting neurong, E2 contains the sample firing of an active neuron, and // # E3 contains the firing of a neuron in an unknown state. // # Based on provided prior probabilities of being in either a resting or active state // # and the fact that neuron firings follow a poisson distribution // # the program calculates the posterior probability ...
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HW6a_solution
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18 Nov 2007 - 15:43 - NEW
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JoshKittleson
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// # This program analyses the sequences in a fasta file, and for each sequence outputs: // # 1) The posterior probability that the sequence was generated using model 1 // # 2) The log ratio of the posterior probabilities (model 1 / model 0) // # where model 0 generates sequences by randomly selecting a nucleotide from the distribution // # of nucleotides in the file and model 1 generates sequences by randomly selecting three // # nucleotides and discarding ...
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HW5_solution
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13 Nov 2007 - 11:03 - NEW
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JoshKittleson
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// # This program processes a stockholm formatted multiple dna/rna alignment // # and then uses the nucleotide distributions over columns and pairs of columns // # to calculate the entropy of each column and the mutual information between // # each pair of columns. // # The columns with the lowest ten entropies are output, as are the pairs // # of columns with the highest 50 mutual informations. // ######Read in the alignment##### // # Get user input // $filename ...
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InformationContentOfDNA
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07 Nov 2007 - 15:22 - r1.126
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JoshKittleson
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// Before we begin // Solutions to hw3a and hw3b are now available. // This lab assumes you are now comfortable navigating through a linux environment and manipulating and using perl files. If you run into basic problems, consult previous labs, a neighbor, or if needed the GSI. // Several new tools are introduced in this lab. Spend a little bit of time familiarizing yourself with them both by reading about them on their source websites, and by tinkering with ...
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BacterialGenePrediction
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29 Oct 2007 - 15:16 - r1.137
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TWikiGuest
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// Bacterial Gene Prediction // Before we begin // The solution to hw4 is posted here. // Goals // Find open reading frames (ORFs) in a bacterial genome // Find the protein translations // Compare different gene prediction methods: // Compare predicted ORFs to "trusted" annotation // Compare to a bacterial genefinding program (Glimmer) // Compare to a translated-protein homology search program (exonerate) // Build experience manipulating genomes and genome annotations ...
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BioE241Presentations
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28 Oct 2007 - 21:36 - r1.54
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TWikiGuest
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// General guidelines // The goals of your presentation should be: // 1 to distil key points of the paper, including salient aspects of the model and of its biological validation (experimental and/or computational); // 1 to identify strengths and limitations of the method, with particular attention to "realism" (pros, cons, improvements, omissions...); // 1 to stimulate discussion, in particular of where this paper sits in relation to the "state-of-the-art" ...
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HW4_solution
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24 Oct 2007 - 17:05 - NEW
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JoshKittleson
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// # This program employs the Needleman-Wunsch algorithm to align two // # strings. It requires as input: // # 1) A matrix file that specifies the similarity matrix for all legal // # characters, and a gap penalty // # 2) A file in fasta format that contains the two sequences to be aligned // # It outputs // # 1) The score matrix for the alignment // # 2) The alignment itself. // #Store user input // $matrixFile $ARGV 0 ; // $sequenceFile $ARGV 1 ; //
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LabSeqAlign
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19 Oct 2007 - 10:32 - r1.61
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TWikiGuest
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// Sequence Alignments // By the end of this lab, you should: // be able to find similar proteins to your protein of interest // have an idea of how to perform sequence alignments using available online tools // know where to look for further help on using these tools // // 0. Before we get started... // We need to have some sequences to work with in this lab. In the Biological Databases lab, we learned how to look up sequence information in one of the many ...
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HW3b_Sol
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14 Oct 2007 - 19:57 - NEW
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JoshKittleson
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// # This program goes through all of the sequences in a fasta file // # and calculates the frequency of C's, G's, and CG dinucleotides // # and then outputs the CG likelihood, p(CG)/p(C)p(G) // # In a genome-wide context, mammals have a far lower occurence of CG dinucleotides than you // # would expect from the C and G nucleotide content alone. Because mammals methylate 70-80 // # of the C's in CG dinucleotides, the high transition mutation rate of methyl cytosine ...
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HW3a_Sol
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14 Oct 2007 - 19:57 - r1.2
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JoshKittleson
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// # This program reads in a fasta file and analyzes if it might be a coding sequence. // # It evaluates three things: // # 1. Does the sequence contain only legitimate nucleotide characters? // # 2. Is the sequence's length is a multiple of 3? // # 3. Is the sequence free of any in frame stop codons? // # The program then outputs // # 1. The sequence name // # 2. The sequence length // # 3. Whether the sequence is a PASS, STOP, or FAIL // # A PASS is output ...
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TempLab
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10 Oct 2007 - 20:02 - r1.60
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JoshKittleson
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// Information content programming exercise // In addition to building on your programming skills, this exercise tests your understanding of the entropy concepts that have been covered in class. // The goal of the exercise is to write a Perl program that does the following (grading shown in red italics ): // 1 Read in a multiple sequence alignment in format (you may assume the file is correctly formatted); (10) // 1 For each column $i$ in the alignment: // 1 ...
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LabRegExp
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08 Oct 2007 - 18:04 - r1.99
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JoshKittleson
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// Pattern Matching in Perl // By the end of this lab, you should know: // how to write some simple regular expressions in Perl // how to read/interpret a regular expression you see in Perl // how to "capture" information from regular expressions // // Before we get started... // In the following lab, we will use a $ symbol to signify a UNIX prompt. The prompt you see in your terminal window may/may not end in a $ , but just remember that you don't actually ...
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BlosumFiftyMatrix
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08 Oct 2007 - 01:18 - NEW
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JoshKittleson
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// A R N D C Q E G H I L K M F P S T W Y V B Z X // 5 2 1 2 1 1 1 0 2 1 2 1 1 3 1 1 0 3 2 0 2 1 1 // 2 7 1 2 4 1 0 3 0 4 3 3 2 3 3 1 1 3 1 3 1 0 1 // 1 1 7 2 2 0 0 0 1 3 4 0 2 4 2 1 0 4 2 3 4 0 1 // 2 2 2 8 4 0 2 1 1 4 4 1 4 5 1 0 1 5 3 4 5 1 1 // 1 4 2 4 13 3 3 3 3 2 2 3 2 2 4 1 1 5 3 1 3 3 2 // 1 1 0 0 3 7 2 2 1 3 2 2 0 4 1 0 1 1 1 3 0 4 1 // 1 0 0 2 3 2 6 3 0 4 3 1 2 3 1 1 1 3 2 3 1 5 1 // 0 3 0 1 3 2 3 8 2 4 4 2 3 4 2 0 2 3 3 4 1 2 2 // 2 0 1 1 3 1 0 2 10 ...
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HW1_Sol2
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06 Oct 2007 - 18:58 - NEW
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JoshKittleson
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// hw2.pl // # hw2.pl compares the contents of two fasta files // # It will note any sequence names that: // # 1) Are present in the first file, but not the second // # 2) Are present in the second file, but not the first // # 3) Are present in both files, but are associated with different sequencess // # Expected input: // # Two filenames for fasta files in valid fasta format // # Produces an error and exits if: // # File names are not entered or not found ...
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HW1_Sol1
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24 Sep 2007 - 17:38 - r1.3
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TWikiGuest
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// # This program reads a fasta file in from a file, and then outputs the reverse complement // # Optionally, it outputs the RNA reverse complement instead of the DNA. // # Syntax for use: hw1.pl filename rna // #Get user input // $filename $ARGV 0 ; // $rnaOption $ARGV 1 ; // #Verify that a file was specified, and that it exists, then open it. // die("You must input a file name!") unless $filename; // die("File doesn't exist!") unless (-e $filename); // open ...
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LabArraysHashes
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24 Sep 2007 - 15:05 - r1.126
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JoshKittleson
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// Arrays and Hashes in Perl // By the end of this lab, you should know: // how to use arrays and hashes in Perl // one way to write the reverse complement exercise // some things to keep in mind when doing error-checking // // 0. Before we get started... // In the following lab, we will use a $ symbol to signify a UNIX prompt. The prompt you see in your terminal window may/may not end in a $ , but just remember that you don't actually type in the $ , just the ...
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NotesForFuture
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20 Sep 2007 - 21:06 - NEW
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JoshKittleson
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// Ok, just a few things here for now. // The solution to the first hw (posted on lab 3) is used as an example in lab 4. The is both a link to a solution posted at the top of the lab 4 page, and a more complex solution developed over the course of the lab. One possible work around: Force students to do hw1 without any data structures or subroutines. The solution imbedded in lab 4 is then useless to them, beyond the kinds of thing already available in the lecture ...
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FrequentlyAskedQuestions
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19 Sep 2007 - 16:46 - r1.22
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JoshKittleson
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// Frequently Asked Questions // I forgot my DECF username or password, I need a cardkey to access the labs afterhours, I need more quota (space) on my account, etc etc. (any other DECF-specific questions) // Please contact the DECF support staff at consult@newton.berkeley.edu. If you're not sure whether a question is appropriate for the DECF staff, email your GSI first. // How can I work on the DECF computers from home? // See the last section of the Teaching ...
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Number of topics: 50
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