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Programming Assignment 4 Computer Science 2 Due Thursday, April 30, 2009 Human genome is made of DNA that consists of sequence of four nucleotide...

Human genome is made of DNA that consists of sequence of four nucleotide bases – A, T, G, and C. In a process called transcription, DNA sequences are transformed to RNA sequences, Transcription keeps all the bases intact to produce RNA from DNA except replacing T’s with U’s. Finally, RNA sequences are translated to protein (amino acids) by combining three nucleotides into codons. Translation follows the following table to synthesize amino acid codons.

Ala/A GCU, GCC, GCA, GCG
Leu/L UUA, UUG, CUU, CUC, CUA, CUG
Arg/R CGU, CGC, CGA, CGG, AGA, AGG
Lys/K AAA, AAG
Asn/N AAU, AAC
Met/M AUG*
Asp/D GAU, GAC
Phe/F UUU, UUC
Cys/C UGU, UGC
Pro/P CCU, CCC, CCA, CCG
Gln/Q CAA, CAG
Ser/S UCU, UCC, UCA, UCG, AGU, AGC
Glu/E GAA, GAG
Thr/T ACU, ACC, ACA, ACG
Gly/G GGU, GGC, GGA, GGG
Trp/W UGG
His/H CAU, CAC
Tyr/Y UAU, UAC
Ile/I AUU, AUC, AUA
Val/V GUU, GUC, GUA, GUG
START AUG*
STOP UAG, UGA, UAA
*replace AUG with an M.

Write an interactive GUI application that has the features as follows:

1. Take input from user either in a text area or by letting him upload a text file with DNA sequences of any length. The format of the sequence is the sequence name followed by the nucleotides.
>Seq1
GCGGCGGGAGCGCGCCCGTTGCAAGATGGCGGCGGCCATGCTGGGCCCCGGGGCTGTGTGTGCGCAGCGGGCGGCGGCGCGGCCCGGAAGGCTGGCGCGGCGAGGCGTTAGCCCGGCCCTCGGCCCCTCTTTGCGGCCGCTCCCTCCGCCTATTCCCTCCTTGCTCGAGATGGATCTGCCCGTGGGCCC

2. Show the transcription to RNA in a text area.
GCGGCGGGAGCGCGCCCGUUGCAAGAUGGCGGCGGCCAUGCUGGGCCCCGGGGCUGUGUGUGCGCAGCGGGCGGCGGCGCGGCCCGGAAGGCUGGCGCGGCGAGGCGUUAGCCCGGCCCUCGGCCCCUCUUUGCGGCCGCUCCCUCCGCCUAUUCCCUCCUUGCUCGAGAUGGAUCUGCCCGUGGGCCC
3. Show the translation of RNA to protein in a text area according to the table above.

AAGARPLQDGGGHAGPRGCVCAAGGGAARKAGAARR.PGPRPLFAAAPSAYSLLARDGSARGP
4. Search the sequences contained in the text file (or typed in the text area) for a user specified sequence (of any length). It should list all sequences (from the list) in which the user specified sequence is a substring, the location at which the substring occurs in each sequence, and the sequence name. Display these information in a text area at the bottom of the GUI. Allow the user to search for as many sequences as desired without having to restart the program.


You may add other features (talk to instructor) and color if you would like. There should also be a button to reset and start over again. You should put your program, all documentation with any directions for the user, substring search algorithm, etc in a folder, then zip it and place it in the drop box
Programming Assignment 4 Computer Science 2 Due Thursday, April 30, 2009 Human genome is made of DNA that consists of sequence of four nucleotide bases – A, T, G, and C. In a process called transcription, DNA sequences are transformed to RNA sequences, Transcription keeps all the bases intact to produce RNA from DNA except replacing T’s with U’s. Finally, RNA sequences are translated to protein (amino acids) by combining three nucleotides into codons. Translation follows the following table to synthesize amino acid codons. Ala/A GCU, GCC, GCA, GCG Leu/L UUA, UUG, CUU, CUC, CUA, CUG Arg/R CGU, CGC, CGA, CGG, AGA, AGG Lys/K AAA, AAG Asn/N AAU, AAC Met/M AUG* Asp/D GAU, GAC Phe/F UUU, UUC Cys/C UGU, UGC Pro/P CCU, CCC, CCA, CCG Gln/Q CAA, CAG Ser/S UCU, UCC, UCA, UCG, AGU, AGC Glu/E GAA, GAG Thr/T ACU, ACC, ACA, ACG Gly/G GGU, GGC, GGA, GGG Trp/W UGG His/H CAU, CAC Tyr/Y UAU, UAC Ile/I AUU, AUC, AUA Val/V GUU, GUC, GUA, GUG START AUG* STOP UAG, UGA, UAA *replace AUG with an M. Write an interactive GUI application that has the features as follows: 1. Take input from user either in a text area or by letting him upload a text file with DNA sequences of any length. The format of the sequence is the sequence name followed by the nucleotides. >Seq1 GCGGCGGGAGCGCGCCCGTTGCAAGATGGCGGCGGCCATGCTGGGCCCCGGGGCTGTGTGTGCGC AGCGGGCGGCGGCGCGGCCCGGAAGGCTGGCGCGGCGAGGCGTTAGCCCGGCCCTCGGCCCCTCT TTGCGGCCGCTCCCTCCGCCTATTCCCTCCTTGCTCGAGATGGATCTGCCCGTGGGCCC 2. Show the transcription to RNA in a text area. GCGGCGGGAGCGCGCCCGUUGCAAGAUGGCGGCGGCCAUGCUGGGCCCCGGGGCUGUGUGUGCGC AGCGGGCGGCGGCGCGGCCCGGAAGGCUGGCGCGGCGAGGCGUUAGCCCGGCCCUCGGCCCCUCU UUGCGGCCGCUCCCUCCGCCUAUUCCCUCCUUGCUCGAGAUGGAUCUGCCCGUGGGCCC 3. Show the translation of RNA to protein in a text area according to the table above. AAGARPLQDGGGHAGPRGCVCAAGGGAARKAGAARR.PGPRPLFAAAPSAYSLLARDGSARGP 4. Search the sequences contained in the text file (or typed in the text area) for a user specified sequence (of any length). It should list all sequences (from the list) in which the user specified sequence is a substring, the location at which the substring occurs in each
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sequence, and the sequence name. Display these information in a text area at the bottom of the GUI. Allow the user to search for as many sequences as desired without having to restart the program. You may add other features (talk to instructor) and color if you would like. There should also be a button to reset and start over again. You should put your program, all documentation with any directions for the user, substring search algorithm, etc in a folder, then zip it and place it in the drop box Grading: Algorithm design 10 points User Friendly GUI 10 points Correct output 80 points as listed above
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