CS 368 Introduction to Bioinformatics Homework 6 (Submit one single zip file including the program and the outputs of the program to D2L Assignments by 10:00PM 4/28/2017)

This is our second programming assignment.

Total: 30 Points

Write a Perl program that prompts for a sequence file name and a motif file name. It will read data from the files and then report the sequence that matches the motif pattern and the position of the match. Recall that the sequence position starts at 1 where as string position starts at 0. The sequence files for ALP are ALP0.txt and ALP.txt. The sequence files for ZF are ZF0.txt and ZF.txt. A motif pattern file contains the regular expression of the motif pattern. The test run and result should look like the following. (Note that pattern matching is not substring searching.)

For ALP0.txt:

Please enter the input sequence file name: ALP0.txt

Please enter the motif pattern file name: pattern_alp.txt

Motif IRDSASTGT found at position 23

For ALP.txt:

Please enter the input sequence file name: ALP.txt

Please enter the motif pattern file name: pattern_alp.txt

Motif VPDSAGTAT found at position 107

For ZF0.txt:

Please enter the input sequence file name: ZF0.txt

Please enter the motif pattern file name: pattern_zf.txt

Motif CSDOCCHICHENGLINPHDTEACH found at position 105

For ZF.txt:

Please enter the input sequence file name: ZF.txt

Please enter the motif pattern file name: pattern_zf.txt

Motif CPYCHRLFSQATHLEVHVRSH found at position 595

Grading

The grade is based on the correctness, robustness, and documentation of the programs.

And I have 4 txt file so I am including that too here

ZF.txt

MPPPTAQFMGPTQAGQNESQNQSSGEAGEQNQEHGQGPTPILNQSQPASSQPQHQQQRNESISYYTNFNQ

PRYSTDASINSFLNISDNVPVTSTGGPSSGGAYSNLPRLSTSSTHQPPDLSQIGRGFSIVNNLFPQQQQL QNQHRQQQQQQQQQSHQQPPFKTPSFSTGLTGSSSQYQFLPRNDNTSQPPSKRNSVYLGPNDGPDFEFFS MQQSQQPQFQPSSRRESNSMRPPLLIPAATTKSQSNGTNNSGNMNTNADYESFFNTGTNNSNSNQNPYFL SSRNNSLKFNPEDFDFQFKRRNSFVRGTLDHSSQNAFIPESRLNSLSVNNKANGDPVADNVTNNMKGKSN EVDNDDGNDSSNNNNNNNNNNNNENNNDNNNDNNDNSINSATSTNIPNQEDHSLASTDTTSNSRKDLKEI EQRLRKHLNDEDNYSSAISRPLDKNDVIEGSEGLNKHIDESGMQPNIIKKRKKDDSTVYVKNEMPRTDPP MSKDNSTSAEGAAMANFSGKEPPIPDISSVSDDATNLIGATKVDQLMLIIQARKKGFTEKVNTTQDGDLL FNQTMDILPPKSELVGGVEKPKGTQNTRAVKKHECPYCHRLFSQATHLEVHVRSHIGYKPFVCDYCGKRF TQGGNLRTHERLHTGEKPYSCDICDKKFSRKGNLAAHLVTHQKLKPFVCKLENCNKTFTQLGNMKAHQNR FHKETLNALTAKLAEMNPSENIPLEERQLLEYFASIYKNSNRGIKGRGKGVGTKKSTISSPENHPASTIL NPNTNANNAIANDSENNGNPEGNIDSSSNSNPGSHSMISPTQKDMGTLQSQFIQNNFNNSVNSSNPSNQP IINYNYTTLPHSRLGSSSSSNTNNNNSNFSVGAAPGVLMAPTTNNDFSFNLDQSNDNERSQQEQVRFKNI NYKS

ZF0.txt

MSKDNSTSAEGAAMANFSGKEPPIPDISSVSDDATNLIGATKVDQLMLIIQARKKGFTEKVNTTQDGDLL FNQTMDILPPKSELVGGVEKPKGTQNTRAVKKHECSDOCCHICHENGLINPHDTEACHIGYKPFVCDYCG TQGGNLRTHERLHTGEKPYSCDICDKKFSRKGNLAAHLVTHQKLKPFVCKLENCNKTFTQLGNMKAH

ALP.txt

MILPFLVLAIGPCLTNSFVPEKEKDPSYWRQQAQETLKNALKLQKLNTNVAKNIIMFLGDGMGVSTVTAA RILKGQLHHNTGEETRLEMDKFPFVALSKTYNTNAQVPDSAGTATAYLCGVKANEGTVGVSAATERTRCN TTQGNEVTSILRWAKDAGKSVGIVTTTRVNHATPSAAYAHSADRDWYSDNEMRPEALSQGCKDIAYQLMH NIKDIDVIMGGGRKYMYPKNRTDVEYELDEKARGTRLDGLDLISIWKSFKPRHKHSHYVWNRTELLALDP SRVDYLLGLFEPGDMQYELNRNNLTDPSLSEMVEVALRILTKNPKGFFLLVEGGRIDHGHHEGKAKQALH EAVEMDEAIGKAGTMTSQKDTLTVVTADHSHVFTFGGYTPRGNSIFGLAPMVSDTDKKPFTAILYGNGPG YKVVDGERENVSMVDYAHNNYQAQSAVPLRHETHGGEDVAVFAKGPMAHLLHGVHEQNYIPHVMAYASCI GANLDHCAWASSASSPSPGALLLPLALFPLRTLF

ALP0.txt

KANEGTVGVSAAKTYNTNCH AQIRDSASTGTAYLCGV