Slides
1. Basic knowledge of Biological sequence and Bioinformatic
http://www.mediafire.com/file/i8rbkh8g3he3beq/Basic_knowledge_of_Biological_sequence_and_Bioinformatic.pdf
2. Biological sequence database
http://www.mediafire.com/file/99c626soflxqx8i/2016_Biological_sequence_DB.pdf
2016-10-25
3. Highlight Sequence Analysis Tools
http://www.mediafire.com/file/oxtols51l8jwido/DNA_analysis2.pdf
4. Similarlity searching and alignment
http://bit.ly/2ewLocw
5. PCR Primer
6. Phylogenetic tree
http://www.mediafire.com/file/gy0ahgsd4ssa59h/Phylogenetic_Tree_Reconstruction_Genome_2016.pdf
7. Informatic of SNPs and Human variation
http://www.mediafire.com/file/idb6a40kb0s5924/The_Informatics_of_SNPs_2016.pdf
8. Haploview
http://www.mediafire.com/file/5ym33c4zc142gm2/Haploview_v4.2.pdf
9. Essential statistic for genomic data
http://www.mediafire.com/file/wflo6646iuvwtcz/Essential_statistic_for_genomic_data.pdf
10. Whole genome and Exome sequencing analysis
http://www.mediafire.com/file/7718epft2i61j5i/Lect2016_WES-NGS.pdf
Assignment 1 : Biological sequence database
Please answer the following question: (ในแต่ละข้อให้ทำการจับภาพและทำการแปะลงบน MS word หรือ MS-powerpoint พร้อมคำอธิบาย) (2 scores each)
1. What is the difference between PubMed and PubMed Central?
2. What is the different between the nucleotide, protein, gene and genome database?
3. Please show step by step to get the sequence in FASTA and GenBank format
4. What is the information you get from the taxonomy database?
5. What is the information you get from any database in the Health session in NCBI database?
The deadline will be 24:00 on 29/10/2016.
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Assignment 3 - Similarity search and alignment
Please choose one sequence from the example file on the link below. Make a similarity search against the sequences in NCBI database. Compare the result between BLASTN and BLASTP, then make a discussion about the result. What do you get from the BLAST result?
Example file
http://www.mediafire.com/view/3ke6ghji71ohdn2/Sequence_assignment3.txt
The deadline will be 24:00 on 13/11/2016.
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Assignment 4 - BioEdit
Please choose one sequence from the example file on the link in assignment 3, then make;
1.sequence complementary
2.six frame translation
3.restriction enzyme analysis
4.make multiple alignment with at least 5 sequences (try to find the related sequence from database with difference genus or species)
5.make consensus sequence with cutoff 60%
The deadline will be 24:00 on 13/11/2016.
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Assignment 6 - Phylogenetic tree
Please make the phylogenetic tree by phylip package using the sequences from assignment 4 and add more sequence upto 10 sequences, then make the discussion.
The deadline will be 24:00 on 27/11/2016.
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Assignment 7 - SNPs
Please use the data from http://www.mediafire.com/file/y48uaatv9ldv3y8/Association.xlsx
Try to prepare the data then use the haploview program, make an analysis and discuss the result espescially the association test.
The deadline will be 24:00 on 30/11/2016.
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