Excel Workshop (2017-04-19)

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Slide:
http://bit.ly/2oJ6mHS

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Excel data files:

http://bit.ly/2oSvj44
http://bit.ly/2petxv5
http://bit.ly/2okNcoO
http://bit.ly/2peyT9k

วิชาเลือก Bioinformatics นักศึกษาแพทย์

Assignment 5 : SNPs

Slide:
http://www.mediafire.com/file/zvsopr8ad0z7p43/The_Informatics_of_SNPs_2016.pdf

Assignment file :
http://www.mediafire.com/file/2518ubxgocz2444/02-Assignment_SNPs_100_SNPs.xlsx

Please use the assignment file from the link to make an analysis using the Haploview program.
Summarize the association result.

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Slide:
http://www.mediafire.com/file/u42bab4eoqu1vse/Bioinformatcis_PDFs_1.zip



Assignment 1.
1.Please show step by step to download the nucleotide sequence in GenBank and FASTA format
2.Please show step by step to download the protein sequence in GenBank and FASTA format

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Assignment 2.
Use the following sequence to make a simailarity search against the sequences on NCBI database. Compare the result between BLASTN and BLASTP, then make the discussion about the result. What do you get from the BLAST result?

>sample1-(smartoat)
GCGGGGGACCTTCGGGCCTCGCGCTATAGGGTTGGCCGATGGCTGATTAGCTAGTTGGTGGGGTAAAGGC
CCACCAAGGCGACGATCAGTAGCTGGTCTGAGAGGACGACCAGCCACACTGGGACTGAGACACGGCCCAG
ACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGCGAAAGCCTGATCCAGCAATGCCGCGTGT
GTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTTGTCCGGAAAGAAATCCTGAGGGCTAATATCCTTCGGG
GATGACGGTACCGGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGA
GCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTTGTTAAGACCGATGTGAAATCCCCGGG
CTCAACCTGGGAACTGCATTGGTGACTGGCAAGCTAGAGTATGGCAGAGGGGGGTAGAATTCCACGTGTA
GCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAAGGCAGCCCCCTGGGCCAATACTGACGCT
CATGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGTCAACT
AGTTGTTGGGGATTCATTTCCTTAGTAACGTAGCTAAC

>sample2-(woman)
AAAGTGATTTTTCATATTTTTCTATTAATGATTCATATTGTAGGGTGATTGCAATGTCATCTAAG
CCATTTACAAGTTTATTTTTCCATGTTTCATCGATATCAAAATGAAAACTTTTATCTGGTGATGACACAG
TTTGATTTGGTAAATCGACCTCAATTTCTACATATTGAGCAAGATGTTCACGTGCACTTTTTTCTAAAAC
AATGGGTAACATCGCATTTTTGGTACAATTCATATAAAAAATGTCACTGAAACTTCCTGCGATGATAATG
TGGAATCCGTAGTCCTTAAGTGCCCAAGCAGCATGTTCGCGACTTGAACCACATCCAAAATTATCACCAG
TAATTAATATGGATGCACCTTTATATTGAGGCTTATTTGGATTGAAATCAGGATTATCTGAACCATCAGG
TAAGTACCGCCATTCATCAAAAGCGAATGGACCAAATCCGCTTTTTGAAATACGTTTTAAATGAACTTTA

>sample3-(poo)
GCTTCCCGATCTTGGCATTACCTCCTTCAAGGTCTTCATGGCCTATCGCGGCATGAACATGATCGACGAC
GTGACGCTGCTGAAGACGCTCGACAAGGCGGTCAAGACCGGATCGCTCGTCATGGTGCACGCGGAAAACG
GCGACGCCGCCGACTATCTGCGCGACAAGTTCGTGGCCGAGGGCAAAACCGCGCCGATCTACCACGCGCT
CAGCCGCCCGCCCCGGGTCGAAGCCGAGGCAACCGCGCGGGCCCTCGCCCTGGCCGAAATCGTCAACGCC
CCGATCTACATAGTCCATGTGACCTGCGAGGAGTCCCTTGAGGAGGTGATGCGCGCAAAATCGCGAGGCG
TCCGCGCTCTGGCGGAAACCTGCACGCATTACCTTTACCTCACCAAGGAAGACCTGGAGCGGCCGGATTT
CGAAGGTGCGAAATACGTTTTCACACCGCCGGCCCGCGCGAAGAAAGACCATGACGTTCTCTGGAACGCA
CTCAGAAACGGTGTGTTCGAAACGGTTTCCTCCGACCATTGCTCCTGGCTCTTCAAGGGGCACAAGGACC
GGGGCCGGAACGACTTTCGCGCCATCCCGAACGGCGCGCCGGGCGTCGAGGAACGGTTGATGATGGTCTA
TCAGGGCGTCAACGAAGGCCGGATTTCCCTTACCCAGTTCGTGGAACTGGTCGCCACGCGCCCGGCCAAG
GTCTTCGGAATGTTTCCGCAAAAGGGGACGATCGCGGTCGGTTCGGACGCCGACATCGTCCTTTGGGACC
CCGAGGCCGAAATGGTGATCGAACAGACCGCCATGCACAACGCCATGGATTACTCCTCCTACGAGGGACA
CAAGGTCAAGGGCGTGCCGAAGACGGTGCTCCTGCGTGGCAAGGTTATC

>sample4-(T-Nai Re)
GTTTTATTAATTTTTGACAAGGAGAATTCTCATGAAACTAGTTAAACTTAGTTTAGTTGCAGCT
CTTGCTGCAGGTGCTTTTTCAGCAGCTAACGCTACTCCACTTGAAGAAGCTATCAAAGATGTTGATGTAT
CAGGTGTATTAAGATACAGATACGATACAGGTAATTTTGATAAAAATTTCGTTAACAACTCAAATTTAAA
CAACAACAAACAAGATCACAAATATAGAGCACAAGTTAACTTCAGTGCTGCTATAGCTGATAACTTCAAA
GCTTTCATTCAGTTTGACTACAACGCTGTTGATGGTGGCACTGGTGTTGATAACGTAACAAATGCCGAAA
AAGGACTTTTTGTTCGTCAATTATACTTAACTTATACAAATGAAGATGTTGCTACAAGTGTAATCGCTGG
TAAACAACAATTAAACCTTATCTGGACGGATAACGCTATTGATGGTTTAGTAGGAACAGGTATCAAAGTA
GTAAACAACAGCATCGATGGTTTAACTCTAGCTGCTTTTGCTGTAGATAGCTTTATGGCGGAAGAGCAAG
GTGCAGATTTATTAGGACAAAGTACTATATCTACAACACAGAAAGCAGCTCCTTTTAAAGTGGATTCAGT
AGGAAATCTTTATGGTGCTGCTGCTGTAGGTTCTTATGATCTTGCTGGCGGACAATTTAATCCACAATTA
TGGTTAGCTTACTGGGATCAAGTAGCATTCTTCTATGCTGTAGATGCAGCTTATAGTACAACTATCTTTG
ATGGAATCAACTGGACACTTGAAGGTGCTTACTTAGGAAATAGCCTT

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Assignment 3.
Please use the sequence from assignment 2 to design the PCR primer (show step by step)

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Assignment 4.

Please use the sequences from the link http://www.mediafire.com/file/0l4b3yqjr271oil/Ass3_phylogenetic_tree.zip

Make the phylogenetic tree, then discuss the output. What is the unknown sequence type?

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