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This week, we're updating our course layouts and descriptions. Presentation and materials always gently change over time, but just occasionally there's a need to make a step change to clear out some of the old and roll in the new. That's now happening - but over a long and complex site it's not instant and you'll see sections of the site changing up to and including 19th September.

See also [here] for status update
 
Converting codons via Amino Acids to Proteins in Perl

DNA is the code of life - a double helix, comprising just four different basic codon elements:
  • Adenine (A)
  • Thymine (T)
  • Guanine (G)
  • Cytosine (c)
and a huge amount of work has gone into analysing these for the genes right across all types of life - including human genes. I understand (but I'm not an expert) that human DNA consists of a string of some 11 billions elements. So it's qute a data handling job to look after this lot and to extract data ... a good way to do that extraction is using the Practical Extraction and Reporting Language (Perl).

Codons are grouped in threes - GGT is one of several codes for the amino acid Glycine, for example; there are around 20 amino acids, and there is a code letter for each of them. G for Glycine, for example.

A group of amino acids then combines to form a protein, with the proteins in any particular DNA string being separated by particular 3-codon sequences with are the major break points - stop codes.

During last week's Perl course, I demonstrated Perl's data handling capability to do this conversion, writing a program from first principles - source code [here]. The conversion of sets of 3 codons to Amino acids uses an unchanging table of data across all sequences, so I've included it within the code file (at the end, not mixed with program lines!). But the sequences will vary - so they're read from separate files; there's an example [here] in industry standard fasta format.

  munchkin:a12perl grahamellis$ perl bacon
  GWG
 
  RCSWRSSGLEQRSRLAATFPRQSARPGRG
 
  APHRRVPRGCSSSGAARGSRWGLGAGPALQDGHSAVSFACLLGQGPEARRAARGEEEGAA
  RGGRGAGGLRGAASGQGRQRREPTQAAVRAHLGAHLEAPGGRVRQEEERQQEGDTQAGIH
  GPRPPGPATQPREPSPQGPGSPRRRRHRQAPGGASAHRARGCRHLRATVGGQRGRSAAGL
  GRGKASAAASPSPAGGAAGAWRLAAAGHRAGVHRRAAALSGRLRVPTLLSPQGAEPGRAG
  GLVPRCGPLAAAAGLARPGLHYACKPGVRVPAVPRVAAWGRAGVGRRAAGRLPHLPLPRL
  LLHGQRDLLPTQALPRGARQGALLAALPAPHPAAQPADAAAQRRPPLLHAGLSRPQERGR
  GRRQRRGPTERGRARRLLGRQGQLRGRNQALDYEPGPLGIPRGRAHPPPQPLTHTRTPRD
  HKATAAVTAAQRPGWAEEETPMPLRGKWRPGHQRPRCLDLLGVEWGRKMSAGKALQPHSS
  RLSAPPFLHFCRGLPLPFSPFPLGFIHFLASFLCLHFSSCLHSSLSLSLSLLFLSFFLPL
  PAFPFSVPWVCVSASPSYPLPDCTP
 
  TPVSPPAPVSPSALLVAPVMCHHLPSCLPSSSTCVSLHFFIPD
 
  VTTPLSPDQREY
 
  FLIWID
 
  GARRNCSPRYPDSHQDGPSPHPHRLSPPFPTCCMLGAGGCGGRGCRLLSGG
 
  GLEAKSTWETTPAAAPQWTGGRKRKLLTLEEGHPASLSLAFLLLLPTAPFNLFGCLRREGGGG
 
  AGPGTVRGAELGRDRNPPGRVPGTELGLGPCPRCQ
 
  CGPTERAALSVCPSVPERTIKRWKRL
  munchkin:a12perl grahamellis$


There are many standard Perl modules that can help with this sort of thing - so you may not want to write your own from scratch (remember - "if you think someone may have done it before, they probably have, and they have probably released the code open source")

If you want to learn how to do it for yourself - perhaps you're researching onwards from these fundamentals - take a look at our range of Perl courses - taking you through from the basics right through to modules on the specialist techniques you might want to employ to handle the huge data sets involved.
(written 2012-04-25, updated 2012-04-28)

 
Associated topics are indexed as below, or enter http://melksh.am/nnnn for individual articles
P212 - Perl - More on Character Strings
  [3927] First match or all matches? Perl Regular Expressions - (2012-11-19)
  [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)
  [3332] DNA to Amino Acid - a sample Perl script - (2011-06-24)
  [3322] How much has Perl (and other languages) changed? - (2011-06-10)
  [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)

P669 - Perl - Data Munging
  [3764] Shell, Awk, Perl of Python? - (2012-06-14)
  [3335] Practical Extraction and Reporting - (2011-06-26)
  [2702] First and last match with Regular Expressions - (2010-04-02)
  [2129] Nothing beats Perl to solve a data manipulation requirement quickly - (2009-04-14)
  [1509] Extracting information from a file of records - (2008-01-16)
  [1316] Filtering and altering Perl lists with grep and map - (2007-08-23)


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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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