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DNA to Amino Acid - a sample Perl script

A really rewarding course this week - Perl programming, for a dozen bright delegates in the bioinformatics field - the people who have defined the human code as billions of C A T and Gs and are then fuzzy matching against that human code to help in medical research. I hope I am forgiven for that simplistic explanation - THEY are the experts at the algorithms, not me. On a course such as this we add their knowledge of the data to my Perl and come up with a glue that is greater than the sum of the components.

The C A T and G letters go together in groups of 3 to make up Amino Acids ... of which there are 24. A hash is a very good way to set up and use this data, and a regular expression substitute is a short (but it must be admitted inefficient) way of translating 3 at a time. Of course, you don't know where in the sequence to start, so there are three possible strings ... see the sample program [here].

I'm sitting in Edinburgh Waverley station this evening, awaiting the sleeper train back to London. Home, midmorning tomorrow. It's been a long week too ...
(written 2011-06-24)

 
Associated topics are indexed as below, or enter http://melksh.am/nnnn for individual articles
P050 - Perl - General
  [3911] How well do you know Perl and / or Python? - (2012-11-04)
  [3902] Shell - Grep - Sed - Awk - Perl - Python - which to use when? - (2012-10-22)
  [3823] Know Python or PHP? Want to learn Perl too? - (2012-07-31)
  [3407] Perl - a quick reminder and revision. Test yourself! - (2011-08-26)
  [3322] How much has Perl (and other languages) changed? - (2011-06-10)
  [3093] How many toilet rolls - hotel inventory and useage - (2010-12-18)
  [2971] Should the public sector compete with businesses? and other deep questions - (2010-09-26)
  [2825] Perl course - is it tailored to Linux, or Microsoft Windows? - (2010-06-25)
  [2783] The Perl Survey - (2010-05-27)
  [2736] Perl Course FAQ - (2010-04-23)
  [2504] Learning to program in ... - (2009-11-15)
  [2374] Lead characters on Perl variable names - (2009-08-24)
  [2242] So what is this thing called Perl that I keep harping on about? - (2009-06-15)
  [2228] Where do I start when writing a program? - (2009-06-11)
  [1897] Keeping on an even keel - (2008-11-21)
  [1750] Glorious (?) 12th August - what a Pe(a)rl! - (2008-08-12)
  [743] How to debug a Perl program - (2006-06-04)
  [400] New in the shops - (2005-08-01)
  [116] The next generation of programmer - (2004-11-13)

P212 - Perl - More on Character Strings
  [3927] First match or all matches? Perl Regular Expressions - (2012-11-19)
  [3707] Converting codons via Amino Acids to Proteins in Perl - (2012-04-25)
  [3650] Possessive Regular Expression Matching - Perl, Objective C and some other languages - (2012-03-12)
  [3630] Serialsing and unserialising data for storage and transfer in Perl - (2012-02-28)
  [3546] The difference between dot (a.k.a. full stop, period) and comma in Perl - (2011-12-09)
  [3411] Single and double quotes strings in Perl - what is the difference? - (2011-08-30)
  [3100] Looking ahead and behind in Regular Expressions - double matching - (2010-12-23)
  [3059] Object Orientation in an hour and other Perl Lectures - (2010-11-18)
  [2993] Arrays v Lists - what is the difference, why use one or the other - (2010-10-10)
  [2877] Further more advanced Perl examples - (2010-07-19)
  [2874] Unpacking a Perl string into a list - (2010-07-16)
  [2834] Teaching examples in Perl - third and final part - (2010-06-27)
  [2801] Binary data handling with unpack in Perl - (2010-06-10)
  [2657] Want to do a big batch edit? Nothing beats Perl! - (2010-03-01)
  [2379] Making variables persistant, pretending a database is a variable and other Perl tricks - (2009-08-27)
  [2230] Running a piece of code is like drinking a pint of beer - (2009-06-11)
  [1947] Perl substitute - the e modifier - (2008-12-16)
  [1735] Finding words and work boundaries (MySQL, Perl, PHP) - (2008-08-03)
  [1727] Equality and looks like tests - Perl - (2008-07-29)
  [1510] Handling Binary data (.gif file example) in Perl - (2008-01-17)
  [1336] Ignore case in Regular Expression - (2007-09-08)
  [1305] Regular expressions made easy - building from components - (2007-08-16)
  [1251] Substitute operator / modifiers in Perl - (2007-06-28)
  [1230] Commenting a Perl Regular Expression - (2007-06-12)
  [1222] Perl, the substitute operator s - (2007-06-08)
  [943] Matching within multiline strings, and ignoring case in regular expressions - (2006-11-25)
  [928] C++ and Perl - why did they do it THAT way? - (2006-11-16)
  [737] Coloured text in a terminal from Perl - (2006-05-29)
  [608] Don't expose your regular expressions - (2006-02-15)
  [597] Storing a regular expression in a perl variable - (2006-02-09)
  [586] Perl Regular Expressions - finding the position and length of the match - (2006-02-02)
  [583] Remember to process blank lines - (2006-01-31)
  [453] Commenting Perl regular expressions - (2005-09-30)


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Efficient travel - from Melsksham to Edinburgh by Sleeper Train
Practical Extraction and Reporting
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Honesty and a friendly welcome goes a long way
DNA to Amino Acid - a sample Perl script
Comparing Alloa and Melksham - stations and services
A lot of exercise this week
Perl from basics
Summer Sundays - days out by train from Swindon on the TransWilts
Why are chefs miserable?
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This is a page archived from The Horse's Mouth at http://www.wellho.net/horse/ - the diary and writings of Graham Ellis. Every attempt was made to provide current information at the time the page was written, but things do move forward in our business - new software releases, price changes, new techniques. Please check back via our main site for current courses, prices, versions, etc - any mention of a price in "The Horse's Mouth" cannot be taken as an offer to supply at that price.

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