The document discusses several topics related to using Perl for bioinformatics lessons including:
- Providing lesson materials and additional educational resources online
- Benefits of using web technology like having questions answered online and avoiding repetitive questions
- Practicum details like introductions, assignments, and locations
- An introduction to the Perl programming language including its history, uses, and advantages for bioinformatics tasks
- Examples of bioinformatics problems that can be solved using Perl like sequence analysis, parsing results, and database queries
The Needleman–Wunsch algorithm is an algorithm used in bioinformatics to align protein or nucleotide sequences. The Needleman–Wunsch algorithm is still widely used for optimal global alignment, particularly when the quality of the global alignment is of the utmost importance.The algorithm essentially divides a large problem (e.g. the full sequence) into a series of smaller problems and uses the solutions to the smaller problems to reconstruct a solution to the larger problem. It is also sometimes referred to as the optimal matching algorithm and the global alignment technique.
Scoring system is a set of values for qualifying the set of one residue being substituted by another in an alignment.
It is also known as substitution matrix.
Scoring matrix of nucleotide is relatively simple.
A positive value or a high score is given for a match & negative value or a low score is given for a mismatch.
Scoring matrices for amino acids are more complicated because scoring has to reflect the physicochemical properties of amino acid residues.
The Needleman–Wunsch algorithm is an algorithm used in bioinformatics to align protein or nucleotide sequences. The Needleman–Wunsch algorithm is still widely used for optimal global alignment, particularly when the quality of the global alignment is of the utmost importance.The algorithm essentially divides a large problem (e.g. the full sequence) into a series of smaller problems and uses the solutions to the smaller problems to reconstruct a solution to the larger problem. It is also sometimes referred to as the optimal matching algorithm and the global alignment technique.
Scoring system is a set of values for qualifying the set of one residue being substituted by another in an alignment.
It is also known as substitution matrix.
Scoring matrix of nucleotide is relatively simple.
A positive value or a high score is given for a match & negative value or a low score is given for a mismatch.
Scoring matrices for amino acids are more complicated because scoring has to reflect the physicochemical properties of amino acid residues.
Automated sequencing of genomes require automated gene assignment
Includes detection of open reading frames (ORFs)
Identification of the introns and exons
Gene prediction a very difficult problem in pattern recognition
Coding regions generally do not have conserved sequences
Much progress made with prokaryotic gene prediction
Eukaryotic genes more difficult to predict correctly
It encloses a brief description of flux balance analysis tools, flux measuring software, methods, advantages and comparable applications to the other software's and analysis techniques and discussion so on steady - constraint based analysis modelling, reconstruction of metabolic pathways and different constraints. etc.
Journal club slides for "Detection of structural DNA variation from next generation sequencing data: a review of informatic approaches" and a description of the software pipeline digit
It is a presentation showing the process of doing a prokaryotic genome annotation using RAST server. It is a basic work in bioinformatics field. Genome annotation is total genome analysis of an organism. We can easily do it using bioinformatics tool like RAST server.
Global and local alignment (bioinformatics)Pritom Chaki
A general global alignment technique is the Needleman–Wunsch algorithm, which is based on dynamic programming. Local alignments are more useful for dissimilar sequences that are suspected to contain regions of similarity or similar sequence motifs within their larger sequence context.
A description of how technology has changed the face of Biology, specially in the fields of genetics, proteomics, and evolution.
It includes a brief history, examples of usage, and a look into the future.
Automated sequencing of genomes require automated gene assignment
Includes detection of open reading frames (ORFs)
Identification of the introns and exons
Gene prediction a very difficult problem in pattern recognition
Coding regions generally do not have conserved sequences
Much progress made with prokaryotic gene prediction
Eukaryotic genes more difficult to predict correctly
It encloses a brief description of flux balance analysis tools, flux measuring software, methods, advantages and comparable applications to the other software's and analysis techniques and discussion so on steady - constraint based analysis modelling, reconstruction of metabolic pathways and different constraints. etc.
Journal club slides for "Detection of structural DNA variation from next generation sequencing data: a review of informatic approaches" and a description of the software pipeline digit
It is a presentation showing the process of doing a prokaryotic genome annotation using RAST server. It is a basic work in bioinformatics field. Genome annotation is total genome analysis of an organism. We can easily do it using bioinformatics tool like RAST server.
Global and local alignment (bioinformatics)Pritom Chaki
A general global alignment technique is the Needleman–Wunsch algorithm, which is based on dynamic programming. Local alignments are more useful for dissimilar sequences that are suspected to contain regions of similarity or similar sequence motifs within their larger sequence context.
A description of how technology has changed the face of Biology, specially in the fields of genetics, proteomics, and evolution.
It includes a brief history, examples of usage, and a look into the future.
An Introduction to Bioinformatics
Drexel University INFO648-900-200915
A Presentation of Health Informatics Group 5
Cecilia Vernes
Joel Abueg
Kadodjomon Yeo
Sharon McDowell Hall
Terrence Hughes
AMC Squarelearning Bangalore is the best training institute for a career development. it had students from various parts of the country and even few were from West African countries.
This is the first set of slightly updated slides from a Perl programming course that I held some years ago for the QA team of a big international company.
I want to share it with everyone looking for intransitive Perl-knowledge.
The updates after 1st of June 2014 are made with the kind support of Chain Solutions (http://chainsolutions.net/)
A table of content for all presentations can be found at i-can.eu.
The source code for the examples and the presentations in ODP format are on https://github.com/kberov/PerlProgrammingCourse
This is an end-to-end introduction to PowerShell, as an interactive shell but more as a scripting language. From the perspective of a full-stack developer, this presentation covers the basics and six of the common issues that occasional users run into.
This is the fourteenth (and last for now) set of slides from a Perl programming course that I held some years ago.
I want to share it with everyone looking for intransitive Perl-knowledge.
A table of content for all presentations can be found at i-can.eu.
The source code for the examples and the presentations in ODP format are on https://github.com/kberov/PerlProgrammingCourse
Custom, in depth 5 day PHP course I put together in 2014. I'm available to deliver this training in person at your offices - contact me at rich@quicloud.com for rate quotes.
Welcome to TechSoup New Member Orientation and Q&A (May 2024).pdfTechSoup
In this webinar you will learn how your organization can access TechSoup's wide variety of product discount and donation programs. From hardware to software, we'll give you a tour of the tools available to help your nonprofit with productivity, collaboration, financial management, donor tracking, security, and more.
Model Attribute Check Company Auto PropertyCeline George
In Odoo, the multi-company feature allows you to manage multiple companies within a single Odoo database instance. Each company can have its own configurations while still sharing common resources such as products, customers, and suppliers.
Synthetic Fiber Construction in lab .pptxPavel ( NSTU)
Synthetic fiber production is a fascinating and complex field that blends chemistry, engineering, and environmental science. By understanding these aspects, students can gain a comprehensive view of synthetic fiber production, its impact on society and the environment, and the potential for future innovations. Synthetic fibers play a crucial role in modern society, impacting various aspects of daily life, industry, and the environment. ynthetic fibers are integral to modern life, offering a range of benefits from cost-effectiveness and versatility to innovative applications and performance characteristics. While they pose environmental challenges, ongoing research and development aim to create more sustainable and eco-friendly alternatives. Understanding the importance of synthetic fibers helps in appreciating their role in the economy, industry, and daily life, while also emphasizing the need for sustainable practices and innovation.
Francesca Gottschalk - How can education support child empowerment.pptxEduSkills OECD
Francesca Gottschalk from the OECD’s Centre for Educational Research and Innovation presents at the Ask an Expert Webinar: How can education support child empowerment?
Read| The latest issue of The Challenger is here! We are thrilled to announce that our school paper has qualified for the NATIONAL SCHOOLS PRESS CONFERENCE (NSPC) 2024. Thank you for your unwavering support and trust. Dive into the stories that made us stand out!
June 3, 2024 Anti-Semitism Letter Sent to MIT President Kornbluth and MIT Cor...Levi Shapiro
Letter from the Congress of the United States regarding Anti-Semitism sent June 3rd to MIT President Sally Kornbluth, MIT Corp Chair, Mark Gorenberg
Dear Dr. Kornbluth and Mr. Gorenberg,
The US House of Representatives is deeply concerned by ongoing and pervasive acts of antisemitic
harassment and intimidation at the Massachusetts Institute of Technology (MIT). Failing to act decisively to ensure a safe learning environment for all students would be a grave dereliction of your responsibilities as President of MIT and Chair of the MIT Corporation.
This Congress will not stand idly by and allow an environment hostile to Jewish students to persist. The House believes that your institution is in violation of Title VI of the Civil Rights Act, and the inability or
unwillingness to rectify this violation through action requires accountability.
Postsecondary education is a unique opportunity for students to learn and have their ideas and beliefs challenged. However, universities receiving hundreds of millions of federal funds annually have denied
students that opportunity and have been hijacked to become venues for the promotion of terrorism, antisemitic harassment and intimidation, unlawful encampments, and in some cases, assaults and riots.
The House of Representatives will not countenance the use of federal funds to indoctrinate students into hateful, antisemitic, anti-American supporters of terrorism. Investigations into campus antisemitism by the Committee on Education and the Workforce and the Committee on Ways and Means have been expanded into a Congress-wide probe across all relevant jurisdictions to address this national crisis. The undersigned Committees will conduct oversight into the use of federal funds at MIT and its learning environment under authorities granted to each Committee.
• The Committee on Education and the Workforce has been investigating your institution since December 7, 2023. The Committee has broad jurisdiction over postsecondary education, including its compliance with Title VI of the Civil Rights Act, campus safety concerns over disruptions to the learning environment, and the awarding of federal student aid under the Higher Education Act.
• The Committee on Oversight and Accountability is investigating the sources of funding and other support flowing to groups espousing pro-Hamas propaganda and engaged in antisemitic harassment and intimidation of students. The Committee on Oversight and Accountability is the principal oversight committee of the US House of Representatives and has broad authority to investigate “any matter” at “any time” under House Rule X.
• The Committee on Ways and Means has been investigating several universities since November 15, 2023, when the Committee held a hearing entitled From Ivory Towers to Dark Corners: Investigating the Nexus Between Antisemitism, Tax-Exempt Universities, and Terror Financing. The Committee followed the hearing with letters to those institutions on January 10, 202
Macroeconomics- Movie Location
This will be used as part of your Personal Professional Portfolio once graded.
Objective:
Prepare a presentation or a paper using research, basic comparative analysis, data organization and application of economic information. You will make an informed assessment of an economic climate outside of the United States to accomplish an entertainment industry objective.
Embracing GenAI - A Strategic ImperativePeter Windle
Artificial Intelligence (AI) technologies such as Generative AI, Image Generators and Large Language Models have had a dramatic impact on teaching, learning and assessment over the past 18 months. The most immediate threat AI posed was to Academic Integrity with Higher Education Institutes (HEIs) focusing their efforts on combating the use of GenAI in assessment. Guidelines were developed for staff and students, policies put in place too. Innovative educators have forged paths in the use of Generative AI for teaching, learning and assessments leading to pockets of transformation springing up across HEIs, often with little or no top-down guidance, support or direction.
This Gasta posits a strategic approach to integrating AI into HEIs to prepare staff, students and the curriculum for an evolving world and workplace. We will highlight the advantages of working with these technologies beyond the realm of teaching, learning and assessment by considering prompt engineering skills, industry impact, curriculum changes, and the need for staff upskilling. In contrast, not engaging strategically with Generative AI poses risks, including falling behind peers, missed opportunities and failing to ensure our graduates remain employable. The rapid evolution of AI technologies necessitates a proactive and strategic approach if we are to remain relevant.
The French Revolution, which began in 1789, was a period of radical social and political upheaval in France. It marked the decline of absolute monarchies, the rise of secular and democratic republics, and the eventual rise of Napoleon Bonaparte. This revolutionary period is crucial in understanding the transition from feudalism to modernity in Europe.
For more information, visit-www.vavaclasses.com
Biological screening of herbal drugs: Introduction and Need for
Phyto-Pharmacological Screening, New Strategies for evaluating
Natural Products, In vitro evaluation techniques for Antioxidants, Antimicrobial and Anticancer drugs. In vivo evaluation techniques
for Anti-inflammatory, Antiulcer, Anticancer, Wound healing, Antidiabetic, Hepatoprotective, Cardio protective, Diuretics and
Antifertility, Toxicity studies as per OECD guidelines
Honest Reviews of Tim Han LMA Course Program.pptxtimhan337
Personal development courses are widely available today, with each one promising life-changing outcomes. Tim Han’s Life Mastery Achievers (LMA) Course has drawn a lot of interest. In addition to offering my frank assessment of Success Insider’s LMA Course, this piece examines the course’s effects via a variety of Tim Han LMA course reviews and Success Insider comments.
3. Bioinformatics.be
• Communiceren van praktische zaken: waar en
wanneer gaan de lessen door
• Ter beschikking stellen van lesmateriaal
• Aanvullend educatief materiaal (FAQ, Web Links)
• Practicum opgaven en programmacode
Voordelen
• Gebruik van het webtechnologie bij het assimileren
van de cursus
• Veel vragen/antwoorden kunnen interessant voor
meerdere mensen, Vermijden van terugkerende
vragen
• Permante discussie (tijdens het jaar) tussen
studenten, prof maar ook thesis en
doctoraatsstudenten
4.
5. Practicum
• Practicum regeling ?
– Inleiding van 45min over de gebruikte editor,
programmeertaal, websites
– 15min toelichting tot de opgaven
– Normaal in PC-zaal D (check bioinformatics.be!)
Perl for Bioinformatics
Part 1: Beginning
Part 2: Mastering
7. • Perl is a High-level Scripting language
• Larry Wall created Perl in 1987
– Practical Extraction (a)nd Reporting
Language
– (or Pathologically Eclectic Rubbish Lister)
• Born from a system administration tool
• Faster than sh or csh
• Sslower than C
• No need for sed, awk, tr, wc, cut, …
• Perl is open and free
• http://conferences.oreillynet.com/e
urooscon/
What is Perl ?
8. • Perl is available for most computing
platforms: all flavors of UNIX (Linux),
MS-DOS/Win32, Macintosh, VMS, OS/2,
Amiga, AS/400, Atari
• Perl is a computer language that is:
– Interpreted, compiles at run-time (need for
perl.exe !)
– Loosely “typed”
– String/text oriented
– Capable of using multiple syntax formats
• In Perl, “there‟s more than one way to do it”
What is Perl ?
9. • Ease of use by novice programmers
• Flexible language: Fast software prototyping (quick
and dirty creation of small analysis programs)
• Expressiveness. Compact code, Perl Poetry:
@{$_[$#_]||[]}
• Glutility: Read disparate files and parse the relevant
data into a new format
• Powerful pattern matching via “regular expressions”
(Best Regular Expressions on Earth)
• With the advent of the WWW, Perl has become the
language of choice to create Common Gateway
Interface (CGI) scripts to handle form submissions
and create compute severs on the WWW.
• Open Source – Free. Availability of Perl modules
for Bioinformatics and Internet.
Why use Perl for bioinformatics ?
10. • Some tasks are still better done with other
languages (heavy computations / graphics)
– C(++),C#, Fortran, Java (Pascal,Visual Basic)
• With perl you can write simple programs
fast, but on the other hand it is also suitable
for large and complex programs. (yet, it is
not adequate for very large projects)
– Python
• Larry Wall: “For programmers, laziness is
a virtue”
Why NOT use Perl for bioinformatics ?
11. • Sequence manipulation and analysis
• Parsing results of sequence analysis
programs (Blast, Genscan, Hmmer etc)
• Parsing database (eg Genbank) files
• Obtaining multiple database entries
over the internet
• …
What bioinformatics tasks are suited to Perl ?
12. Example of problems we will be solving
• Primary Sequence analysis
• Perform alignments
• Simulation experiments to explain
Blast statistics
• Predicting protein topology
• Predicting secondary structures
• “Real-life” problems
– Proteomics: Given aa masses find protein
in database
– …
13. • Perl (op USB):
– Perl is available for various operating systems. To
download Perl and install it on your computer, have a
look at the following resources:
– www.perl.com (O'Reilly).
• Downloading Perl Software
– ActiveState. ActivePerl for Windows, as well as for
Linux and Solaris.
• ActivePerl binary packages.
– CPAN
• http://www.bioinformatics.be/n
ew/faq/setup/
Perl installation
14. Check installation
• Command-line flags for perl
– Perl – v
• Gives the current version of Perl
– Perl –e
• Executes Perl statements from the comment
line.
– Perl –e “print 42;”
– Perl –e “print ”Twonlinesn”;”
– Perl –we
• Executes and print warnings
– Perl –we “print „hello‟;x++;”
15. How to enter your first program ?
• Gebruik een editor
– DOS: EDIT
– Windows:
• NOTEPAD (Let op!)
• Word(Pad) -> TEXT FILE
– Scite:
http://www.scintilla.org/SciTE.html
– Textpad
– Others
• VIM
• Eclipse
16. Path:
Route followed by OS to
locate, save, and/or
retrieve a file
Brief Introduction to Subdirectories—The Path
17. • Probleem
– Ofwel kan je perl starten
– Ofwel kan je het script niet vinden
– Ofwel kan je een file nodig in het script niet
vinden
• Oplossing
– Don‟t panic !
– Gebruikt absolute path-namen
• D:Perlbinperl.exe D:tempTest.pl
– Let wel in je script met je de slash “escape”
• $filename = “d:Temppdb.fasta”
Het absolute pad probleem …
18. • Oplossingen (II)
– Kopieer al de files in dezelfde directory !
– Dus als je perl start vanuit D:Perlbin met perl
kan je wel verwijzen naar D:Temptest.pl maar
dan moet ook de absolute verwijzing gebruikt
worden voor $filename ofwel moet je pdb.fasta
copieren naar D:PerlBin
– Pas het zoekpad aan zodat je perl overal kan
starten
• Path (geeft het zoekpad)
• Set Path (past het pad aan, Voorzichtig !). Gebruik de
dos environment variabele %path% om een directory
toe te voegen
• Set path=%path%;d:Perlbin
• (nadien kan de aanpassing controleren door “path” uit
te voeren)
19. Keyboard:
Standard input device
Screen:
Standard output device
Redirection
Redirection . . .
changes output from monitor to
somewhere else (usually file or
printer).
20. Textpad
Minimal install: via Minerva save file
textpad.be to your folder. Create
system folder in the same location. In
system folder save plumb.exe
(Minerva) and perl syntax files
(textpad.com)
• Syntax Highlighting
– Document Class
• Launch Perl
– Tools
22. • Perl is mostly a free format language: add
spaces, tabs or new lines wherever you
want.
• For clarity, it is recommended to write
each statement in a separate line, and use
indentation in nested structures.
• Comments: Anything from the # sign to
the end of the line is a comment. (There
are no multi-line comments).
• A perl program consists of all of the Perl
statements of the file taken collectively as
one big routine to execute.
General Remarks
23. How does the real perl program look like:
#!/usr/local/bin/perl
print “Hello everyonen”;
Mandatory first line (on UNIX)
How to run it:
1. Save the text of your code as a file -- program.pl
2. Execute it:
perl program.pl
Hello everyone
24. Three Basic Data Types
• Scalars - $
• Arrays of scalars - @
• Associative arrays of
scalers or Hashes - %
26. Ok, $c is 4. How do we know it?
print “Hello n”;
print command:
$c = 4;
print “$c”;
“ ” - bracket output expression
n - print a end-of-the-line character
(equivalent to pressing ‘Enter’)
print “Hello everyonen”;
print “Hello” . ” everyone” . “n”;
Strings concatenation:
Expressions and strings together:
print “2 + 2 = “ . (2+2) . ”n”;
expression
2 + 2 = 4
27. Loops and cycles (for statement):
# Output all the numbers from 1 to 100
for ($n=1; $n<=100; $n+=1) {
print “$n n”;
}
1. Initialization:
for ( $n=1 ; ; ) { … }
2. Increment:
for ( ; ; $n+=1 ) { … }
3. Termination (do until the criteria is satisfied):
for ( ; $n<=100 ; ) { … }
4. Body of the loop - command inside curly brackets:
for ( ; ; ) { … }
28. FOR & IF -- all the even numbers from 1 to 100:
for ($n=1; $n<=100; $n+=1) {
if (($n % 2) == 0) {
print “$n”;
}
}
Note: $a % $b -- Modulus
-- Remainder when $a is divided by $b
29. Two brief diversions (warnings & strict)
• Use warnings
• strict – forces you to „declare‟ a variable the
first time you use it.
– usage: use strict; (somewhere near the top of
your script)
• declare variables with „my‟
– usage: my $variable;
– or: my $variable = „value‟;
• my sets the „scope‟ of the variable. Variable
exists only within the current block of code
• use strict and my both help you to debug
errors, and help prevent mistakes.
30. Unary Arithmetic Operators eg. Autoincrement ++
• If you place one of the auto operators before the variable, it is
known as a pre-incremented (pre-decremented) variable. Its
value will be changed before it is referenced. If it is placed
after the variable, it is known as a post-incremented (post-
decremented) variable and its value is changed after it is used
For example:
• $a = 5; # $a is assigned 5
• $b = ++$a; # $b is assigned the incremented value of $a, 6
• $c = $a--; # $c is assigned 6, then $a is decremented to 5
#!e:perlbinperl.exe
• $getal1 = 5;
• print $getal1."n";
• print $getal1++."n";
• print ++$getal1."n";
31. Logical and Comparison operators
• Equal (True if $a is equal to $b)
– Numeric: ==
– String: eq
• And: &&
• Or: ||
33. Text Processing Functions
The substr function
• Definition
• The substr function extracts a substring out of a
string and returns it. The function receives 3
arguments: a string value, a position on the string
(starting to count from 0) and a length.
Example:
• $a = "university";
• $k = substr ($a, 3, 5);
• $k is now "versi" $a remains unchanged.
• If length is omitted, everything to the end of the
string is returned.
34. Random
#!c:perlbinperl.exe -w
#srand(time|$$);
$x = rand(1);
• srand
– The default seed for srand, which used to be time, has
been changed. Now it's a heady mix of difficult-to-predict
system-dependent values, which should be sufficient for
most everyday purposes. Previous to version 5.004,
calling rand without first calling srand would yield the
same sequence of random numbers on most or all
machines. Now, when perl sees that you're calling rand
and haven't yet called srand, it calls srand with the default
seed. You should still call srand manually if your code
might ever be run on a pre-5.004 system, of course, or if
you want a seed other than the default
35. • Oefening hoe goed zijn de random
nummers ?
• Als ze goed zijn kan je er Pi mee
berekenen …
• Een goede random generator is
belangrijk voor goede
randomsequenties die we nadien
kunnen gebruiken in simulaties