Difference between revisions of "Bioinformatics homework"

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<p><strong><span style="font-size:18px">Jong Bhak&#39;s Bioinformatics homework</span></strong></p>
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<p><span style="font-size:20px"><strong>Jong Bhak&#39;s Bioinformatics homework </strong></span><span style="font-size:18px"><strong>(for any bioinforamtics students)</strong></span></p>
  
<p><strong>1. Learn Perl programming language</strong></p>
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<p>&nbsp;</p>
  
<p><strong>2. Watch the following YouTube lectures;</strong></p>
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<p><span style="font-size:18px"><strong>1. Learn [[Perl]] programming language and learn bioinformatics using it.</strong></span></p>
  
<p>&nbsp; &nbsp;[https://www.youtube.com/watch?v=lJzybEXmIj0 MIT Bioinforamtics intro]</p>
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<ul>
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<li><span style="font-size:16px">[[Install and Learn BioPerl]]</span></li>
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<li><span style="font-size:16px">[[Make a Perl program translating &#39;all&#39; combinations of triple bases into amino acids]]</span></li>
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<li><span style="font-size:16px">[[Make a Perl program to calculate the lengths of DNA and protein sequences]]</span></li>
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<li><span style="font-size:16px">[[Make a Perl program to calculate the length of a Mycoplasma genitalium bacterium]]</span></li>
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<li><span style="font-size:16px">[[Pick 5 protein sequences and predict their secondary structures using available prediction programs]]</span></li>
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<li><span style="font-size:16px">[[Open and re-write one FASTA file containing one protein sequence of TERT]]</span></li>
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<li><span style="font-size:16px">[[Create a FASTA file with a sequence. Open it and reverse the sequence of it and print it out in another FASTA file]]</span></li>
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<li><span style="font-size:16px">[[Extract a sequence MKKTGIKG from ASMKATAHQMKKTGIKGMSTYALLRL and print it out in a file]] </span></li>
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<li><span style="font-size:16px">[[In a multi-sequence FASTA file, produce statistics&nbsp;such as sequence number, average seq length, GC content, AT content, etc]]</span></li>
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<li><span style="font-size:16px">[[Align two protein sequences using a dynamic programming method in Perl]]</span></li>
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<li><span style="font-size:16px">[[Randomly generate five 100 AA long protein sequences and store them in a FASTA file]]</span></li>
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<li><span style="font-size:16px">[[Create a flat text file database of protein sequences with hash function in Perl]]</span></li>
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</ul>
  
<p>&nbsp; &nbsp;[https://www.youtube.com/watch?v=6Udqou3vmng Chris Burge&#39;s local alignment lecture from MIT] &nbsp;&nbsp;</p>
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<p>&nbsp;</p>
  
<p>&nbsp; &nbsp;[https://www.youtube.com/watch?v=PdyARRNwi7I&nbsp;Chris Burge&#39;s alignment lecture from MIT]</p>
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<p>&nbsp;</p>
  
<p>&nbsp; &nbsp;[https://www.youtube.com/watch?v=ZYW2AeDE6wU Genome Assembly from MIT]</p>
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<p><span style="font-size:18px"><strong>2. Learn various bioinformatics program and tasks</strong></span></p>
  
<p>&nbsp; &nbsp;[https://www.youtube.com/watch?v=P3ORBMon8aw David Gifford MIT&nbsp;Library Complexity and Short Read Alignment]</p>
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<ul>
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<li>[[Access&nbsp;http://koreanreference.org/home/index.html and search for TERT_HUMAN DNA region]]</li>
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<li><span style="font-size:16px">[[Install a sequence alignment viewer program on your computer]]</span></li>
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<li><span style="font-size:16px">[[Install a protein 3D structure viewer program on your computer]]</span></li>
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<li><span style="font-size:16px">[[Create a MySQL database and add 5 protein sequences in your MySQL DB]]</span></li>
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<li>[[Download TERT_HUMAN sequence and search for 3D structure of it and build a 3D model using bat&#39;s TERT homolog sequence using the human 3D template]]</li>
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<li>[[Access http://string-db.org/&nbsp; and find all the interaction partners of TERT_HUMAN protein]]</li>
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<li>[[How to use NCBI database to construct a protein sequence]]</li>
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</ul>
  
<p>&nbsp; &nbsp;[https://www.youtube.com/watch?v=Ob9xGBPvr_s Chip-seq analyses + DNA protein interaction from MIT]</p>
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<p>&nbsp;</p>
  
<p>&nbsp; &nbsp;[</p>
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<p><span style="font-size:18px"><strong>3. Watch the following YouTube lectures;</strong></span></p>
 +
 
 +
<p><span style="font-size:16px">&nbsp; &nbsp;</span><span style="font-size:14px">MIT 생정보연구자들의 시리즈</span></p>
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 +
<p><span style="font-size:14px">&nbsp; &nbsp;[https://www.youtube.com/watch?v=lJzybEXmIj0 MIT Bioinforamtics intro] </span></p>
 +
 
 +
<p><span style="font-size:14px">&nbsp; &nbsp;[https://www.youtube.com/watch?v=6Udqou3vmng Chris Burge&#39;s local alignment lecture from MIT] &nbsp;&nbsp;</span></p>
 +
 
 +
<p><span style="font-size:14px">&nbsp; &nbsp;[https://www.youtube.com/watch?v=PdyARRNwi7I&nbsp;Chris Burge&#39;s alignment lecture from MIT]</span></p>
 +
 
 +
<p><span style="font-size:14px">&nbsp; &nbsp;[https://www.youtube.com/watch?v=ZYW2AeDE6wU Genome Assembly from MIT]</span></p>
 +
 
 +
<p><span style="font-size:14px">&nbsp; &nbsp;[https://www.youtube.com/watch?v=P3ORBMon8aw David Gifford MIT&nbsp;Library Complexity and Short Read Alignment]</span></p>
 +
 
 +
<p><span style="font-size:14px">&nbsp; &nbsp;[https://www.youtube.com/watch?v=Ob9xGBPvr_s Chip-seq analyses + DNA protein interaction from MIT]</span></p>
 +
 
 +
<p><span style="font-size:14px">&nbsp; &nbsp;[https://www.youtube.com/watch?v=MniYgsZSp30 &nbsp;RNA-seq analyses by MIT David Gifford]</span></p>
 +
 
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<p><span style="font-size:14px">&nbsp; &nbsp;[https://www.youtube.com/watch?v=1EMonM7qAU8 Modelling and discovery of sequence motifs by MIT]</span></p>
 +
 
 +
<p><span style="font-size:14px">&nbsp; &nbsp;[https://www.youtube.com/watch?v=d5NMrA2HkG4 Markov and Hidden Markov models for genome and protein sequence features]</span></p>
 +
 
 +
<p><span style="font-size:14px">&nbsp; &nbsp;[https://www.youtube.com/watch?v=kUN6rJ21Hno RNA-sequence secondary structures by MIT]</span></p>
 +
 
 +
<p><span style="font-size:14px">&nbsp; &nbsp;[https://www.youtube.com/watch?v=6ROBp57G2ZI Intro to protein structure and comparisons]</span></p>
 +
 
 +
<p><span style="font-size:14px">&nbsp; &nbsp;[https://www.youtube.com/watch?v=j1s9JfZKFqU Predicting protein structure from MIT]</span></p>
 +
 
 +
<p><span style="font-size:14px">&nbsp; &nbsp;[https://www.youtube.com/watch?v=C95294_vvQY Predicting protein-protein interactions]</span></p>
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 +
<p><span style="font-size:14px">&nbsp; &nbsp;[https://www.youtube.com/watch?v=So6MK_FcP4E Gene regulartory networks by MIT]</span></p>
 +
 
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<p><span style="font-size:14px">&nbsp; &nbsp;[https://www.youtube.com/watch?v=RBPcKbEvK3U Protein interaction networks by MIT]</span></p>
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<p><span style="font-size:14px">&nbsp; &nbsp;[https://www.youtube.com/watch?v=i59JDQ9hk10 Logic modeling of cell signalling networks by MIT]</span></p>
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<p><span style="font-size:14px">&nbsp; &nbsp;[https://www.youtube.com/watch?v=iKLvCuFD1MA Analysis of chromatic structure by MIT]</span></p>
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<p><span style="font-size:14px">&nbsp; &nbsp;[https://www.youtube.com/watch?v=kx_Hks_-SZM Discoverying quantitative trait loci by MIT]</span></p>
 +
 
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<p><span style="font-size:14px">&nbsp; &nbsp;[https://www.youtube.com/watch?v=KYQ2dPW5nEU Human genetics SNPs, GWAS by MIT]</span></p>
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<p><span style="font-size:14px">&nbsp; &nbsp;[https://www.youtube.com/watch?v=kKyrR0cFrEg Synthetic biology by MIT]</span></p>
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 +
<p><span style="font-size:14px">&nbsp; &nbsp;[https://www.youtube.com/watch?v=uD4-fOWeXAY Causality, Natural language and genome engineering]</span></p>
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 +
<p><span style="font-size:14px">&nbsp; &nbsp;[https://www.youtube.com/watch?v=0E0a5ZaE6Gk George Church&#39;s future of genomics and synthetic biology]</span></p>
 +
 
 +
<p><span style="font-size:14px">&nbsp; &nbsp;[https://www.youtube.com/watch?v=SuAxDVBt7kQ Genome Engineering by Jennifer Doudnaby UC Berkeley] 제니퍼 다우드나의 강의</span></p>
 +
 
 +
<p>&nbsp;</p>
 +
 
 +
<hr />
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<p>[http://biolecture.org/index.php/UNIST_Bioinformatics_course UNIST Bioinformatics course]</p>
 +
 
 +
<p>[http://bioinformatics.ws 생정보학 전반에 대한 온라인 홈페이지]</p>

Latest revision as of 14:42, 7 May 2018

Jong Bhak's Bioinformatics homework (for any bioinforamtics students)

 

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

 

 

2. Learn various bioinformatics program and tasks

 

3. Watch the following YouTube lectures;

   MIT 생정보연구자들의 시리즈

   MIT Bioinforamtics intro

   Chris Burge's local alignment lecture from MIT   

   Burge's alignment lecture from MIT

   Genome Assembly from MIT

   David Gifford MIT Library Complexity and Short Read Alignment

   Chip-seq analyses + DNA protein interaction from MIT

    RNA-seq analyses by MIT David Gifford

   Modelling and discovery of sequence motifs by MIT

   Markov and Hidden Markov models for genome and protein sequence features

   RNA-sequence secondary structures by MIT

   Intro to protein structure and comparisons

   Predicting protein structure from MIT

   Predicting protein-protein interactions

   Gene regulartory networks by MIT

   Protein interaction networks by MIT

   Logic modeling of cell signalling networks by MIT

   Analysis of chromatic structure by MIT

   Discoverying quantitative trait loci by MIT

   Human genetics SNPs, GWAS by MIT

   Synthetic biology by MIT

   Causality, Natural language and genome engineering

   George Church's future of genomics and synthetic biology

   Genome Engineering by Jennifer Doudnaby UC Berkeley 제니퍼 다우드나의 강의

 


UNIST Bioinformatics course

생정보학 전반에 대한 온라인 홈페이지