Difference between revisions of "Homework"

From Biolecture.org
imported>Yeong Jae Kim
imported>Yeong Jae Kim
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<p><strong>1. Learn&nbsp;<a href="http://biolecture.org/index.php/Perl" title="Perl">Perl</a>&nbsp;programming language and learn bioinformatics using it.</strong></p>
 
<p><strong>1. Learn&nbsp;<a href="http://biolecture.org/index.php/Perl" title="Perl">Perl</a>&nbsp;programming language and learn bioinformatics using it.</strong></p>
  
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<p>&nbsp;[[1) Install and Learn Bioperl]]&nbsp;</p>
+
<p>&nbsp;[[1.&nbsp;Install and Learn Bioperl]]&nbsp;</p>
  
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<p>&nbsp;[[2) Make a perl program translating &#39;all&#39; combinations of triple bases into amino acids]]</p>
+
<p>&nbsp;[[2.&nbsp;Make a perl program translating &#39;all&#39; combinations of triple bases into amino acids]]</p>
  
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<p>&nbsp;[[3) Pick 5 protein sequences and predict their secondary structures using available prediction programs]]</p>
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<p>&nbsp;[[3.&nbsp;Pick 5 protein sequences and predict their secondary structures using available prediction programs]]</p>
  
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<p>&nbsp;[[4) Open and re-write one FASTA file containing one protein sequence of TERT]]</p>
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<p>&nbsp;[[4.&nbsp;Open and re-write one FASTA file containing one protein sequence of TERT]]</p>
  
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<p>&nbsp;[[5) Create a FASTA file with a sequence. Open it and reverse the sequence of it and print it out in another FASTA file]]</p>
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<p>&nbsp;[[5.&nbsp;Create a FASTA file with a sequence. Open it and reverse the sequence of it and print it out in another FASTA file]]</p>
  
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<p>&nbsp;[[6) Extract a sequence MKKTGIKG from ASMKATAHQMKKTGIKGMSTYALLRL and print it out in a file]]</p>
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<p>&nbsp;[[6.&nbsp;Extract a sequence MKKTGIKG from ASMKATAHQMKKTGIKGMSTYALLRL and print it out in a file]]</p>
  
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<p>&nbsp;[[7) In a multi-sequence FASTA file, produce statistics such as sequence number, average seq length, GC content, AT content, etc]]</p>
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<p>&nbsp;[[7.&nbsp;In a multi-sequence FASTA file, produce statistics such as sequence number, average seq length, GC content, AT content, etc]]</p>
  
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<p>&nbsp;[[8) Align two protein sequences using a dynamic programming method in perl]]</p>
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<p>&nbsp;[[8.&nbsp;Align two protein sequences using a dynamic programming method in perl]]</p>
  
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<p>&nbsp;[[9) Randomly generate five 100 AA long protein sequences and store them in a FASTA file]]</p>
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<p>&nbsp;[[9.&nbsp;Randomly generate five 100 AA long protein sequences and store them in a FASTA file]]</p>
  
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<p>&nbsp;[[10) Create a flat text file database of protein sequences with has functino in Perl]]</p>
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<p>&nbsp;[[10.&nbsp;Create a flat text file database of protein sequences with has functino in Perl]]</p>
  
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>

Revision as of 19:53, 17 May 2016

1. Learn Perl programming language and learn bioinformatics using it.

 1. Install and Learn Bioperl 

 2. Make a perl program translating 'all' combinations of triple bases into amino acids

 3. Pick 5 protein sequences and predict their secondary structures using available prediction programs

 4. Open and re-write one FASTA file containing one protein sequence of TERT

 5. Create a FASTA file with a sequence. Open it and reverse the sequence of it and print it out in another FASTA file

 6. Extract a sequence MKKTGIKG from ASMKATAHQMKKTGIKGMSTYALLRL and print it out in a file

 7. In a multi-sequence FASTA file, produce statistics such as sequence number, average seq length, GC content, AT content, etc

 8. Align two protein sequences using a dynamic programming method in perl

 9. Randomly generate five 100 AA long protein sequences and store them in a FASTA file

 10. Create a flat text file database of protein sequences with has functino in Perl

 

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