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Transcript 
Homework 2.2
 What is your understanding of Bioinformatics?
 Which fields or problems of Bioinformatics are you
interest in?
Homework 2.3
 Search and download the mRNA and Protein
sequences of gene TP53 (human&mouse) from NCBI
 Analyze the number of A, T, C, G, respectively
 Analyze the number of different codons, respectively
Homework 3.1
 Search and download the mRNA and Protein
sequences of gene TP53(human&mouse) from NCBI
 Alignment the mRNA sequences using Pairwise
Sequence Alignment in:
 Alignment the Protein sequences using Pairwise
Sequence Alignment in:
http://www.ebi.ac.uk/Tools/psa/
 Compare the results of Global Alignment and Local
Alignment
Homework 3.2
 Make gene prediction of the provided sequence using
more than one approaches, and compare the
prediction results.
Homework 3.2
>mgutLn1_U_BL_aaa09a01_b1 Mouse Gut Community PT3 :
mgutLn1_U_BL_aaa09a01_b1
GTTAACTATCTCGCCCTGTGGTGGATTCTCATTGAACCGAAGCGGACAGG
ATTCCGGGTGTCGTCGTTGTCGCCGTCGGGGGACTGATACAGCGGGAGGT
CAGTGAAAGCCTTGTCTGCCTGATTGACGCGCTGCCACCTTGATAATGCT
TTGGCCACGAATTCCCGTGGCGATTCCTCCATATTGTCGAATAGACAACT
TGCCGAACCCCTGGAAGATTGCGCTTGCAGTATGTAGGGATATTGACCTG
CAGTTGCACCGGGATTGATCCTGATGCGCTTTACACAGGCTGGAGATACC
CGGAATCTTCCAACGCAAGTGGCGTAATATTGGGTAATCTGCTCTTAGTT
TCAGGTTTTCAGATTAGGGACAACCCCGAATCCCCCCTGGTCTCTGCGGC
GAATCCTCGCAGACTAAGCCACCGAGATGTGTTCGACCTTACATGATTAG
TGCGCTCTTACCCTCGCCGAGGTATATCATGCAAAAAATATGCAATGAAA
AACACTGTTGATGCTATATGATATGACCGCTCTGATGACTCTTTACGAAC
CCCCGAATAGGCGCTGCGCATGGATAACTGGGAAAACATTCTTTCCGTCA
TGCTGTCAGAGTTGCTCCAGAACGTTCGGCCTCGGAACACCGACCACTGT
AACAATGGCTGAGACGCCGAAAACTCCCAAAACAGGAACGTGTCTTAACC
TA
Homework 3.2
 homology-based approaches
 http://bibiserv.techfak.uni-bielefeld.de/agenda/
 ab initio
 Glimmer:
http://www.ncbi.nlm.nih.gov/genomes/MICROBES/glimmer
_3.cgi
 GeneMark
http://exon.gatech.edu/
 wiki
http://en.wikipedia.org/wiki/Gene_prediction#Comparative_g
enomics_approaches
Homework 3.3
 Make Motif prediction of the downloaded protein
sequence of human TP53 in homework3.1 using more
than one approaches, and compare the prediction
results.
 Find the Motifs from last step in protein sequences of
mouse TP53 by yourself. (The Motif maybe not in
protein of mouse TP53)
Homework 3.4
 Provide one explanation of why an arbitrarily composed
DNA sequence generally does not have the barcode
properties of genomic DNA sequences?
 Run the barcode server at
http://csbl1.bmb.uga.edu/Barcode/Barcode.html on the
DNAseq of Escherichia coli. What information can you
derive from the barcode image of the sequence?
Homework 4.1
 Find a reputable structure prediction server and make a tertiary
structure prediction of the following sequence.
FVFQQSEKFAKVENQYQLLKLETNEFQQLQSKISLISEKLESTESILQEATSSMSLMTQF
EQEVSNLQDIMHDIQNNEEVLTQRMQSLNEKFQNITDFWKRSLEEMNINTDIFKSEAKHI
HSQVTVQINSAEQEIKLLTERLKDLEDSTLRNIRTVKRQEEEDLLRVEEQLGSDTKAIEK
LEEEQHALFARDEDLTNKLSDYEPKVEECKTHLPTIESAIHSVLRVSQDLIETEKKMEDL
TMQMFNMEDDMLKAVSEIMEMQKTLEGIQYDNSILKMQNELDILKEKVHDFIAYSSTGEK
GTLKEYNIENKGIGGDF
 wiki：
http://en.wikipedia.org/wiki/List_of_protein_structure_prediction_software
Homework 4.2
 Give a detailed report on known functions, structures,
etc on a protein family of Pfam that starts with “A”
Homework 4.2
 Write a search report on a specific protein, say cpiB,
based on your search results against GO database
http://www.geneontology.org/
Homework 5.1
 Find one popular program for prediction of co-expressed
genes based on microarray expression data on the Internet.
Explain its basic idea.
 Qserver:
http://csbl.bmb.uga.edu/publications/materials/ffzhou/QServer/
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