CPE 101: Fundamentals of Computer Science I
Lab 8

Executables

dotplot01-alex executable for dotplot01.c program
dotplot02-alex executable for dotplot02.c program
iconvert-alex executable for iconvert.c program
dna2amino-alex executable for dna2amino.c program
palindrome-alex executable for palindrome.c program
seq2ppm-alex executable for seq2ppm.c program

Test Data

These tests are to get you started

dotplot01.c, dotplot02.c

plot-test01 plot1.ppm: dotplot01.c output plot1-3.ppm: dotplot02.c oupout
plot-test02 plot2.ppm: dotplot01.c output plot2-3.ppm: dotplot02.c oupout
plot-test03 plot3.ppm: dotplot01.c output plot3-3.ppm: dotplot02.c oupout

icomplement.c, dna2ppm.c, palindrom.c

dna-tests.tar.gzall tests
dna-test01
dna-test02
dna-test03
dna-test04
dna-test05
dna-test06
dna-test07
dna-test08
dna-test09
dna-test10

seq2ppm.c
seq-test01 seq1.ppm: output
seq-test02 seq2.ppm: output
seq-test03 seq2.ppm: output

Real Data

This data comes from various on-line genome sequence databases

dotplot01.c, dotplot02.c

plot-tests.tar.gz: All tests (1 -- 15)

Input File dotplot01 output dotplot02 output Origin
plot-test04 plot04.ppm plot04-3.ppm (matching) fragments of two influenza (H1N1) viruses (2009 strain)
plot-test05 plot05.ppm plot05-3.ppm (matching) fragments of two influenza (H1N1) viruses (2009 strain)
plot-test06 plot06.ppm plot06-3.ppm (matching) fragments of two influenza (H1N1) viruses (2009 strain)
plot-test07 plot07.ppm plot07-3.ppm (matching) fragments of two influenza (H1N1) viruses (2009 strain)
plot-test08 plot08.ppm plot08-3.ppm (matching) fragments of two influenza (H1N1) viruses (2009 strain)
plot-test09 plot09.ppm plot09-3.ppm ribosomal protein S3: human vs. chimpanzee
plot-test10 plot10.ppm plot10-3.ppm ribosomal protein S3: human vs. dog
plot-test11 plot11.ppm plot11-3.ppm ribosomal protein S3: human vs. mouse
plot-test12 plot12.ppm plot12-3.ppm ribosomal protein S3: human vs. moscito
plot-test13 plot13.ppm plot13-3.ppm fragment of HD protein (Huntington's disease) vs. itself
plot-test14 plot14.ppm plot14-3.ppm forkhead box P2 (regulates transcription in brain development)
fragment: human vs. chmpanzee
plot-test15 plot15.ppm plot15-3.ppm fragments (nucleotides) of two influenza viruses

icomplement.c, dna2ppm.c, palindrom.c

Fragments of influenza A (H1N1) virus.

dna-fragments.tar.gzall tests
dna-fragment01
dna-fragment02
dna-fragment03
dna-fragment04
dna-fragment05
dna-fragment06
dna-fragment07
dna-fragment08
dna-fragment09
dna-fragment10

seq2ppm.c

Tests 4-9 - fragments of 10 strains of Influenza A (2008 and 2009 versions).
Test 10: synthetic.
seq-tests.tar.gzall tests
seq-test04 sq4.ppm
seq-test05 sq5.ppm
seq-test06 sq6.ppm
seq-test07 sq7.ppm
seq-test08 sq8.ppm
seq-test09 sq9.ppm
seq-test10 sq10.ppm


September 11, 2009 dekhtyar at calpoly.edu