Practical Bioinformatics Mark Voorhies 5/ 24/ 2013 Mark Voorhies - PowerPoint PPT Presentation

Jan 24, 2024 •313 likes •401 views

Practical Bioinformatics Mark Voorhies 5/ 24/ 2013 Mark Voorhies Practical Bioinformatics Clustering exercises { Visualizing the distance matrix Mark Voorhies Practical Bioinformatics Scripting Cluster Running Cluster3 from the command line

Practical Bioinformatics Mark Voorhies 5/ 24/ 2013 Mark Voorhies Practical Bioinformatics
Clustering exercises { Visualizing the distance matrix Mark Voorhies Practical Bioinformatics
Scripting Cluster Running Cluster3 from the command line / Applications/ Cluster.app/ Contents/ MacOS/ Cluster / Program Files/ Stanford University/ Cluster3/ Cluster.com Command-line programs are like functions \ man program" is like \ help(function)" Use the subprocess module to run command-line programs from within Python. Mark Voorhies Practical Bioinformatics
Programs as functions USAGE: cluster [options] -f filename File loading -u jobname Allows you to specify a different name for the output files (default is derived from the input file name) -g [0..8] Specifies the distance measure for gene clustering 0: No gene clustering 1: Uncentered correlation 2: Pearson correlation 3: Uncentered correlation, absolute value 4: Pearson correlation, absolute value 5: Spearman’s rank correlation 6: Kendall’s tau 7: Euclidean distance 8: City-block distance (default: 0) -m [msca] Specifies which hierarchical clustering method to use m: Pairwise complete-linkage s: Pairwise single-linkage c: Pairwise centroid-linkage a: Pairwise average-linkage (default: m) Mark Voorhies Practical Bioinformatics
Scripting the Protocol from s u b p r o c e s s import c h e c k c a l l c h e c k c a l l ( # Which program to run ( ” c l u s t e r ” , # Input f i l e ” − f ” , ” supp2data . tdt ” , # Output p r e f i x ” − u” , ” supp2data . Uncentered . Complete ” , # C l u s t e r i n g method : complete l i n k a g e ” m” , ”m” , − # Distance f u n c t i o n : uncentered Pearson ” − g” , ”1” )) Mark Voorhies Practical Bioinformatics
Using the Cluster3 GUI Mark Voorhies Practical Bioinformatics
Load your data Mark Voorhies Practical Bioinformatics

Recommend

Practical Bioinformatics Mark Voorhies 5/22/2015 Mark Voorhies Practical Bioinformatics PAM

Practical Bioinformatics Mark Voorhies 5/22/2015 Mark Voorhies Practical Bioinformatics PAM (Dayhoff) and BLOSUM matrices PAM1 matrix originally calculated from manual alignments of highly conserved sequences (myoglobin, cytochrome C, etc.)

979 views • 71 slides

Practical Bioinformatics Mark Voorhies 5/15/2015 Mark Voorhies Practical Bioinformatics

Practical Bioinformatics Mark Voorhies 5/15/2015 Mark Voorhies Practical Bioinformatics Gotchas Indentation matters Mark Voorhies Practical Bioinformatics Clustering exercises Visualizing the distance matrix Mark Voorhies Practical

705 views • 46 slides

Practical Bioinformatics Mark Voorhies 4/16/2018 Mark Voorhies Practical Bioinformatics

Practical Bioinformatics Mark Voorhies 4/16/2018 Mark Voorhies Practical Bioinformatics JavaTreeView link-out for ENSEMBL Mouse http://www.ensembl.org/Mus musculus/Gene/Summary?g=HEADER Mark Voorhies Practical Bioinformatics Science! Mark

767 views • 20 slides

Practical Bioinformatics Mark Voorhies 5/23/2019 Mark Voorhies Practical Bioinformatics

Practical Bioinformatics Mark Voorhies 5/23/2019 Mark Voorhies Practical Bioinformatics JavaTreeView link-out for ENSEMBL Mouse http://www.ensembl.org/Mus musculus/Gene/Summary?g=HEADER Mark Voorhies Practical Bioinformatics Science! Mark

330 views • 13 slides

Practical Bioinformatics Mark Voorhies 5/21/2019 Mark Voorhies Practical Bioinformatics Change

Practical Bioinformatics Mark Voorhies 5/21/2019 Mark Voorhies Practical Bioinformatics Change of Coordinates http://xkcd.com/123/ Mark Voorhies Practical Bioinformatics Principal Components Analysis (PCA) Is there a point of view that

264 views • 11 slides

Practical Bioinformatics Mark Voorhies 5/26/2015 Mark Voorhies Practical Bioinformatics Habits

Practical Bioinformatics Mark Voorhies 5/26/2015 Mark Voorhies Practical Bioinformatics Habits are things you get for free, without requiring any special work. Cory Doctorow Advice to Writers, 4/5/2012 Mark Voorhies Practical

521 views • 27 slides

Practical Bioinformatics Mark Voorhies 5/11/2015 Mark Voorhies Practical Bioinformatics

Introduction to Python Practical Bioinformatics Mark Voorhies 5/11/2015 Mark Voorhies Practical Bioinformatics Introduction to Python Good ideas shamelessly lifted from David Erle and Josh Pollack Mark Voorhies Practical Bioinformatics

718 views • 46 slides

Practical Bioinformatics Mark Voorhies 4/9/2018 Mark Voorhies Practical Bioinformatics

Practical Bioinformatics Mark Voorhies 4/9/2018 Mark Voorhies Practical Bioinformatics Clustering exercises Visualizing the distance matrix Mark Voorhies Practical Bioinformatics Dictionaries d i c t i o n a r y = { A : T ,

77 views • 5 slides

Practical Bioinformatics Mark Voorhies 5/14/2019 Mark Voorhies Practical Bioinformatics Course

Practical Bioinformatics Mark Voorhies 5/14/2019 Mark Voorhies Practical Bioinformatics Course platform: VirtualBox Host operating system (e.g., OS X) VirtualBox Debian Linux Web 8888 8088 Jupyter Browser launches Python3 Bash Bash

756 views • 32 slides

Practical Bioinformatics Mark Voorhies 4/19/2011 Mark Voorhies Practical Bioinformatics Review

Practical Bioinformatics Mark Voorhies 4/19/2011 Mark Voorhies Practical Bioinformatics Review Topic Learning Python Dive Into Python Types (string, int, float, list) 2 3 Assignment (=, +=) 2 3 Slicing and indexing 4 3.2 References

443 views • 6 slides

Practical Bioinformatics Mark Voorhies 4/29/2011 Mark Voorhies Practical Bioinformatics Our

Practical Bioinformatics Mark Voorhies 4/29/2011 Mark Voorhies Practical Bioinformatics Our current tool set data (strings, floats, lists, nested lists) logic (if/then, try/except, for, while) functions (def, import, reload) Mark Voorhies

615 views • 25 slides

Practical Bioinformatics Mark Voorhies 5/29/2019 Mark Voorhies Practical Bioinformatics

Practical Bioinformatics Mark Voorhies 5/29/2019 Mark Voorhies Practical Bioinformatics Example Pipeline: Overview Mark Voorhies Practical Bioinformatics Example Pipeline: Overview Generate Genome Transfer Pre-process Samples Coverage

521 views • 16 slides

Practical Bioinformatics Mark Voorhies 5/19/2015 Mark Voorhies Practical Bioinformatics Review

Practical Bioinformatics Mark Voorhies 5/19/2015 Mark Voorhies Practical Bioinformatics Review Documentation A program should communicate its intent to both the computer and human programmers. Comments Docstrings Mark Voorhies

495 views • 26 slides

Practical Bioinformatics Mark Voorhies 5/31/2013 Mark Voorhies Practical Bioinformatics

Practical Bioinformatics Mark Voorhies 5/31/2013 Mark Voorhies Practical Bioinformatics Exercise: Scoring a gapped alignment 1 Given two equal length gapped sequences (where - represents a gap) and a scoring matrix, calculate an

335 views • 5 slides

Practical Bioinformatics Mark Voorhies 4/2/2018 Mark Voorhies Practical Bioinformatics

Introduction to Python Practical Bioinformatics Mark Voorhies 4/2/2018 Mark Voorhies Practical Bioinformatics Introduction to Python Resources Course website: http://histo.ucsf.edu/BMS270/ Resources on the course website: Syllabus Papers

660 views • 37 slides

Practical Bioinformatics Mark Voorhies 4/24/2017 Mark Voorhies Practical Bioinformatics

Introduction to Python Practical Bioinformatics Mark Voorhies 4/24/2017 Mark Voorhies Practical Bioinformatics Introduction to Python Resources Course website: http://histo.ucsf.edu/BMS270/ Resources on the course website: Syllabus Papers

701 views • 43 slides

Practical Bioinformatics Mark Voorhies 5/13/2019 Mark Voorhies Practical Bioinformatics

Introduction to Python Practical Bioinformatics Mark Voorhies 5/13/2019 Mark Voorhies Practical Bioinformatics Introduction to Python Resources Course website: http://histo.ucsf.edu/BMS270/ Resources on the course website: Syllabus Papers

594 views • 42 slides

Practical Bioinformatics Mark Voorhies 4/6/2017 Mark Voorhies Practical Bioinformatics Loading

Practical Bioinformatics Mark Voorhies 4/6/2017 Mark Voorhies Practical Bioinformatics Loading and re-loading your functions # Use import the f i r s t time you load a module # (And keep using import u n t i l i t loads # s u c c

775 views • 32 slides

Practical Bioinformatics Mark Voorhies 5/12/2015 Mark Voorhies Practical Bioinformatics

Practical Bioinformatics Mark Voorhies 5/12/2015 Mark Voorhies Practical Bioinformatics Gotchas Strings are quoted, names of things are not. mystring = mystring Mark Voorhies Practical Bioinformatics Gotchas Strings are quoted,

554 views • 27 slides

Practical Bioinformatics Mark Voorhies 5/21/2013 Mark Voorhies Practical Bioinformatics

Practical Bioinformatics Mark Voorhies 5/21/2013 Mark Voorhies Practical Bioinformatics Gotchas Enclosing symbols (,,(),[],...) need to be matched Mark Voorhies Practical Bioinformatics Gotchas Enclosing symbols

99 views • 7 slides

Practical Bioinformatics Mark Voorhies 4/20/2011 Mark Voorhies Practical Bioinformatics Review

Practical Bioinformatics Mark Voorhies 4/20/2011 Mark Voorhies Practical Bioinformatics Review Corrected slides for days 1 and 2 are on the website Mark Voorhies Practical Bioinformatics Review Corrected slides for days 1 and 2 are on the

248 views • 10 slides

Practical Bioinformatics Mark Voorhies 4/28/2017 Mark Voorhies Practical Bioinformatics

Practical Bioinformatics Mark Voorhies 4/28/2017 Mark Voorhies Practical Bioinformatics Pearson distances Pearson similarity N i ( x i x offset )( y i y offset ) s ( x , y ) = N N i ( x i x offset ) 2 i ( y i

502 views • 28 slides

Intro to NGS Theoretical and Practical HiC Workshop: Wet-lab and Bioinformatics November 4th,

Intro to NGS Theoretical and Practical HiC Workshop: Wet-lab and Bioinformatics November 4th, 2019 Selene L. Fernndez-Valverde regRNAlab.github.io @SelFdz 1 Learning objectives In this class we will learn How high-throughput (NGS)

728 views • 30 slides

Algorithms in Bioinformatics: A f Practical Introduction Practical Introduction Peptide

Algorithms in Bioinformatics: A f Practical Introduction Practical Introduction Peptide Sequencing Peptide Sequencing What is Peptide Sequencing? g High-throughput Protein Sequencing is to deduce the amino acid sequence of a d d h i

669 views • 53 slides