Genome informatics 2016

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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Assignment for Bioinformatic in molecular technique (2016)

An emerging infectious disease (EID) is an infectious disease whose incidence has increased in the past 20 years and could increase in the near future. EIDs are caused by SARS, MERS, Influenza virus, Zika virus and Ebola virus.

Please chose one of the EIDs viruses above.
1. Download the set of sequences at least 5 sequences from different source/counties.
2. Make the consensus sequence of the set of sequences using a threshold of consensus as 60%.
3. Translate the set of the sequence to amino acid sequence then make the phylogenetic tree and discuss the result.

Show step by step to do the assignment.
The deadline for the assignment will be Midnight 9/oct/2016.

An Overview of Bioinformatics

An Overview of Bioinformatics
Basic knowledge of sequence data
Sequence Database
-NCBI
-Reference sequence
-Genome
-Gene
-Taxonomy
-Sequence retrieval

Sequence Analysis Tools
-DNA-DNA-RNA
-Complementary, Reverse complementary
-Restriction enzyme map
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Sequence Comparison Tools
-Pairwise alignment
-Multiple alignment
-Consensus sequence
-Contig assembly

Bioedit

Primer & Probe Design

Phylogenetic reconstruct

Sequence submission