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Bioinformatics homework

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<p~~><strong~~>Jong Bhak's Bioinformatics homework(for any bioinforamtics students)

1. Learn [[Perl ]] programming languageand learn bioinformatics using it. <ul> <li>[[Install and Learn BioPerl]]</li> <li>[[Make a Perl program translating 'all' combinations of triple bases into amino acids]]</li> <li>[[Make a Perl program to calculate the lengths of DNA and protein sequences]]</li> <li>[[Make a Perl program to calculate the length of a Mycoplasma genitalium bacterium]]</li> <li>[[Pick 5 protein sequences and predict their secondary structures using available prediction programs]]</li> <li>[[Open and re-write one FASTA file containing one protein sequence of TERT]]</li> <li>[[Create a FASTA file with a sequence. Open it and reverse the sequence of it and print it out in another FASTA file]]</li> <li>[[Extract a sequence MKKTGIKG from ASMKATAHQMKKTGIKGMSTYALLRL and print it out in a file]] </li> <li>[[In a multi-sequence FASTA file, produce statistics such as sequence number, average seq length, GC content, AT content, etc]]</li> <li>[[Align two protein sequences using a dynamic programming method in Perl]]</li> <li>[[Randomly generate five 100 AA long protein sequences and store them in a FASTA file]]</li> <li>[[Create a flat text file database of protein sequences with hash function in Perl]]</li></ul>     2. Learn various bioinformatics program and tasks <ul> <li>[[Access http://koreanreference.org/home/index.html and search for TERT_HUMAN DNA region]]</li> <li>[[Install a sequence alignment viewer program on your computer]]</li> <li>[[Install a protein 3D structure viewer program on your computer]]</li> <li>[[Create a MySQL database and add 5 protein sequences in your MySQL DB]]</li> <li>[[Download TERT_HUMAN sequence and search for 3D structure of it and build a 3D model using bat's TERT homolog sequence using the human 3D template]]</li> <li>[[Access http://string-db.org/  and find all the interaction partners of TERT_HUMAN protein]]</li> <li>[[How to use NCBI database to construct a protein sequence]]</li></ul>

23. Watch the following YouTube lectures;

~~[https:~~</~~/www.youtube.com/watch?v~~span>MIT ~~Bioinforamtics intro]~~생정보연구자들의 시리즈

[https://www.youtube.com/watch?v=~~6Udqou3vmng Chris Burge's local alignment lecture from~~ lJzybEXmIj0 MITBioinforamtics intro] ~~  ~~

[https://www.youtube.com/watch?v=~~PdyARRNwi7I ~~6Udqou3vmng Chris Burge's local alignment lecture from MIT]

[https://www.youtube.com/watch?v=~~ZYW2AeDE6wU Genome Assembly~~ PdyARRNwi7I Chris Burge's alignment lecture from MIT]

[https://www.youtube.com/watch?v=~~P3ORBMon8aw David Gifford~~ ZYW2AeDE6wU Genome Assembly from MIT~~ Library Complexity and Short Read Alignment~~]

[https://www.youtube.com/watch?v=~~Ob9xGBPvr_s Chip-seq analyses + DNA protein interaction from~~ P3ORBMon8aw David Gifford MIT Library Complexity and Short Read Alignment]

[https://www.youtube.com/watch?v=~~MniYgsZSp30  RNA~~Ob9xGBPvr_s Chip-seq analyses by + DNA protein interaction from MIT ~~David Gifford~~]

[https://www.youtube.com/watch?v=~~1EMonM7qAU8 Modelling and discovery of sequence motifs~~ MniYgsZSp30  RNA-seq analyses by MITDavid Gifford]

[https://www.youtube.com/watch?v=~~d5NMrA2HkG4 Markov and Hidden Markov models for genome~~ 1EMonM7qAU8 Modelling and ~~protein~~ discovery of sequence ~~features~~motifs by MIT]

[https://www.youtube.com/watch?v=~~kUN6rJ21Hno RNA-~~d5NMrA2HkG4 Markov and Hidden Markov models for genome and protein sequence ~~secondary structures by MIT~~features]

[https://www.youtube.com/watch?v=~~6ROBp57G2ZI Intro to protein structure and comparisons~~kUN6rJ21Hno RNA-sequence secondary structures by MIT]

[https://www.youtube.com/watch?v=~~j1s9JfZKFqU Predicting~~ 6ROBp57G2ZI Intro to protein structure ~~from MIT~~and comparisons]

[https://www.youtube.com/watch?v=~~C95294_vvQY~~ j1s9JfZKFqU Predicting protein~~-protein interactions~~structure from MIT]

[https://www.youtube.com/watch?v=~~So6MK_FcP4E Gene regulartory networks by MIT~~C95294_vvQY Predicting protein-protein interactions]

[https://www.youtube.com/watch?v=~~RBPcKbEvK3U Protein interaction~~ So6MK_FcP4E Gene regulartory networks by MIT]

[https://www.youtube.com/watch?v=~~i59JDQ9hk10 Logic modeling of cell signalling~~ RBPcKbEvK3U Protein interaction networks by MIT]

[https://www.youtube.com/watch?v=~~iKLvCuFD1MA Analysis~~ i59JDQ9hk10 Logic modeling of ~~chromatic structure~~ cell signalling networks by MIT]

[https://www.youtube.com/watch?v=~~kx_Hks_-SZM Discoverying quantitative trait loci~~ iKLvCuFD1MA Analysis of chromatic structure by MIT]

[https://www.youtube.com/watch?v=~~KYQ2dPW5nEU Human genetics SNPs, GWAS~~ kx_Hks_-SZM Discoverying quantitative trait loci by MIT]

[https://www.youtube.com/watch?v=~~kKyrR0cFrEg Synthetic biology~~ KYQ2dPW5nEU Human genetics SNPs, GWAS by MIT]

[https://www.youtube.com/watch?v=~~uD4-fOWeXAY Causality, Natural language and genome engineering~~kKyrR0cFrEg Synthetic biology by MIT]

[https://www.youtube.com/watch?v=~~0E0a5ZaE6Gk George Church's future of genomics~~ uD4-fOWeXAY Causality, Natural language and ~~synthetic biology~~genome engineering]

[https://www.youtube.com/watch?v=0E0a5ZaE6Gk George Church's future of genomics and synthetic biology]    [https://www.youtube.com/watch?v=SuAxDVBt7kQ Genome Engineering by Jennifer Doudnaby UC Berkeley]제니퍼 다우드나의 강의

<hr />

[http://biolecture.org/index.php/UNIST_Bioinformatics_course UNIST Bioinformatics course]

[http://bioinformatics.ws 생정보학 전반에 대한 온라인 홈페이지]

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