1. BINF 634 Fall 2013 - Lecture 14 Review 1 Final Review Lec 1 Review of Molecular Biology –Central dogma –Proteins –DNA –Reading frames Perl topics: Running perl variables: scalars, arrays, hashes while loops Scalar and list context string operations –printing –substitution: s/x/y/ –translation: tr/abc/def/ Lec 2 Input / output String operations –concatentation, quoting String functions –length, split, join, substr, index, sprintf, uc, lc, chomp Array Functions Conditionals Logical operators Loops Finding motifs Counting nucleotides

2. BINF 634 Fall 2013 - Lecture 14 Review 2 Final Review Lec 3 Perl Shortcuts Declaring variables and Scope Subroutines Array References Programming Methods –Top Down Design –Bottom Up Coding and Testing –Pseudocode Reading manuals and help pages Debugging POD Lec 4 Logical expression string functions: substr and index Random numbers and mutation Hashes Transcription, translation, genetic code –Implementation using hashes

3. BINF 634 Fall 2013 - Lecture 14 Review 3 Final Review Lec 5 Regular expressions Meta-characters Controlling patterns –|, *, +, {N,M}, ? Capturing matches –$`, $&, $' –$1, $2 … –($x, $y) = $s =~ /(…) … (…)/ –g modifier Lec 6 Data Structures and Efficiency /usr/bin/time head, tail, diff, cmp Hashes for effiecient lookup and counting –Intersection –Unique items in two lists –Counting items Sorting –using BLOCKS –using user-defined subroutines sort LIST sort BLOCK LIST sort USERSUB LIST

4. BINF 634 Fall 2013 - Lecture 14 Review 4 Final Review Lec 7 Functions on arrays –splice, grep, map Two-dimensional arrays –Processing –Printing –Transposing Using Hashes to Pass Parameters to subroutines Lec 8 Perl Modules Module Getopt::Std Range Operator Restriction Maps Parsing Rebase File

5. BINF 634 Fall 2013 - Lecture 14 Review 5 Final Review Lec 9 CGI.pm Creating HTML pages with Perl Forms processing A general Web front end for Perl programs Security in CGI Programming –Taint mode -T –Untainting user supplied data –Using external programs Permissions issued –cgi-bin directory –Using temporary directories Lec 10: SQL and MySQL Tables Column Types and Properties Keys, Indexes, and AUTO_INCREMENT The mysql client Creating databases and tables Inserting records Selecting data Using conditionals Using LIKE and NOT LIKE Sorting query results Limiting query results Updating data Deleting data Using functions Perl DBI

6. BINF 634 Fall 2013 - Lecture 14 Review 6 Final Review Lec 11 Data Visualization –GD::Graph –gnuplot Lec 12 Advanced SQL for Multiple Table Databases –JOINS Objected Oriented Perl –Objects –Attributes –Methods –Classes –Instances Intro to BioPerl –Bio::Seq –Bio::SeqIO –Bio::DB::GenBank –Bio::Perl

7. BINF 634 Fall 2013 - Lecture 14 Review 7 Final Review Lec 13 Adding links to CGI script Command Line Perl –perl -e –perl -ne –perl -ane –BEGIN {}, END {} Environmental variables and the ENV hash Files and Directories –opendir, readdir, closedir, mkdir, rmdir, chdir –File test operators -r -w -x -o -e -s -f -d Recursion XML Lec 14 Final Review Course readings: Tisdall: –Chapters 1-12 –Appendix B Wall: –Chapters 1, 5, 26 –pp 579-584 –Ch 24: Common Practices (recommended)

8. BINF 634 Fall 2013 - Lecture 14 Review 8 Final Review Take Home Final Exam –No collaboration allowed on the exam. –Due to me via email by 7:15 pm Monday 12/16/13 –No extensions will be given –Good Luck! 1.Barplot in GD (See Visualization Lecture) 2.Barplots in GD on a Directory Structure (See Cmd Line Recursion Lecture) 3.Shaded Pattern in GD (See http://search.cpan.org/~lds/GD-2.46/GD.pm, think about the order that you draw things in)http://search.cpan.org/~lds/GD-2.46/GD.pm 4.PubMed XML Processing (See the Cmd Recursion Record) 5.File extraction and conversion with Bioperl (See Bioperl Lecture) 6.LWP (See http://search.cpan.org/~gaas/libwww-perl-6.03/lib/LWP.pm)http://search.cpan.org/~gaas/libwww-perl-6.03/lib/LWP.pm) 7.Bioperl Sequence Manipulations (See BioPerl Lecture) 8.Barplots in PDL see hint and visualization lecture 9.Piecharts in R see tonight’s lecture 10.Please try to provide me answers based on your real needs when possible.

9. Additional Reading Mastering Perl for Bioinformatics [Paperback] –James D. Tisdall (Author) Building Bioinformatics Solutions: with Perl, R and MySQL [Paperback] –Conrad Bessant (Author), Ian Shadforth (Author), Darren Oakley(Author) BINF 634 Fall 2013 - Lecture 14 Review9

10. Thanks to each and everyone of you to taking this course with me! Perseverance is the hard work you do after you get tired of doing the hard work you already did. Newt Gingrich Read more at http://www.brainyquote.com/quotes/quotes/n/newtgingri1 07062.html#Ayx6LpiuIl4lAZfR.99http://www.brainyquote.com/quotes/quotes/n/newtgingri1 07062.html#Ayx6LpiuIl4lAZfR.99 BINF 634 Fall 2013 - Lecture 14 Review10

11. Advertisement for Spring 2012 BINF702 – RESEARCH METHODS (3 Credit Hours) –Noncalculus-based biostatistics –Statistical analysis and programming with R –MONDAY 7:20 pm – 10:00 pm –Has a distance learning section BINF704-COLLOQUIUM (1 Credit Hour) –Tuesday 4:30-6:00pm BINF705-RESEARCH ETHICS (1 Credit Hour) –Tuesday 6:00 pm – 7:00 pm BINF734-ADVANCED BIOINFORMATICS PROGRAMMING (3 Credit Hours) –Tuesdays 7:20 pm – 10:00 pm –Jason Kinser BINF 634 Fall 2013 - Lecture 14 Review11

12. Course Evaluation Evaluate my course by using the MyMason Portal listed below. –http://myMason.gmu.edu/http://myMason.gmu.edu/ –Closing dates 12/10/11 regular sections 12/9/11 distance learning section –Training slides are provided at the url below https://crserating.gmu.edu/CourseEvaluation.ppt The evaluations are important to me and the university. You must must use their Mason Net ID and password to access the system. The survey is not available between 6 pm on Sundays and 6 am on Mondays due to server maintenance. BINF 634 Fall 2013 - Lecture 14 Review12