BINP13, Programming in Perl

BINP13 - Exercises page

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Here are files and stuff needed for the different exercises.
You can also find the lecture notes split into different chapters.

Lecture notes and other files

Lecture notes		Program header and a documented example
Chapt 0-2		prog_header.txt
Chapt 3		lotto.perl
Chapt 4
Chapt 5		Introduction perl script
Chapt 6		intro.perl
Appendix
Old exams		Misc Perl scripts
exam13.pdf exam13-sol.pdf exam14.pdf exam14-sol.pdf		summaryChapt3.perl - sortExamples.perl - misc1.perl - misc2.perl - misc3.perl - misc4.perl - misc5.perl - misc6.perl - fun1.perl - fun2.perl - fun3.perl

Follow-up exercises

Follow-up exercises	Files to download	Perl scripts in the lecture notes
Chapt 3	F3-3: numbers.txt F3-5: protein_sequences.fasta - multiply.perl	fread.perl - fwrite.perl - fappend.perl - hsort.perl - codons.perl codons2.perl - codons3.perl

Chapt 4	F4-1: protein_sequences.fasta (the same as above!) F4-3: sprotseq.perl	splitfasta.perl - splitfasta2.perl - splitwhite.perl - map1.perl - map2.perl - subend.perl - subpar.perl - subsum.perl - subsums.perl - sumfn.perl - sumnfn.perl - sumnfn2.perl - sumnfn3.perl - popchop.perl - popchop2.perl - countwords.perl - scansprot2.perl - sum.perl - sum2.perl

Chapt 5	F5-1: convert-missing.perl - clustalw1.aln - clustalw2.aln - phylip1.aln - phylip2.aln F5-2: ref2.perl - ref3.perl F5-3: search.perl - PDB-table.txt - pdb_seqres.txt - mkindex.perl - pdb2sprot.txt - sprot-subset2.dat F5-4: parse.perl - 1TEN_blastp.res	ref4.perl - ref5.perl - dub_words2.perl

Chapt 6	F6-1: matrix.dat F6-2: cgi1.perl - cgi2.perl - cgi3.perl - cgi4.perl - cgi5.perl NOTE! You have to rename the cgi* programs to end with .pl and not with .perl F6-3: bp_ex1.perl - bp_ex2.perl - bp_ex3.perl - seqs.fasta F6-4: bp_ex4.perl - bp_ex5.perl - bp_ex7.perl - bp_ex8.perl - 1TEN.fasta - 1TEN_blastp.res - phylip1.align - 1TEN_fasta.res	matrix1.perl - matrix2.perl - matrix2r.perl - matrix3.perl rnd1.perl - rnd2.perl - stat1.perl - pdl1.perl Some documentation for the different modules used. CGI.pdf - bioPerl_howto.pdf - seqio_howto.pdf

Hand-in Exercises

Hand-in #	Files to download	Sample outputs **	Send your files to
1 (chapt 3)	H1: aminos.txt H2: protseq.txt H3: 1ECD.fasta	sample-H1-1.txt sample-H1-2.txt sample-H1-3.txt sample-H1-4.txt	andre@thep.lu.se
2 (chapt 4)	H1: elegans.swissprot H2: ecoli.fasta - translation.txt	sample-elegans.fasta sample-terminal.txt sample-ecoli.fasta	mattias@thep.lu.se
3 (chapt 5)	H2: 1TEN_fasta.res	sample-1TEN_fasta.txt	andre@thep.lu.se
4 (chapt 6)	H1: ldb1.gb - ldb2.gb H2: dengue_virus_4.gb	sample-ldb1.txt - sample-ldb2.txt sample-dengue.txt	mattias@thep.lu.se

** For some of the hand-in exercises these sample outputs are for guidance, for some they define
the output of your own program.

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This page was created in May, 2004.
Available at http://home.thep.lu.se/~mattias/teaching/bnf072/binp13_exercises.html.
Latest update: October 22, 2015.