Kristoffer Chin: Week 8

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Chapter 2

  • The first task is to retrieve the protein sequence of the HIV gp120 using the website http://www.expasy.org/sprot/ as previously instructed in the Bioinformatics for Dummies book.
  • Using the search option, i typed in HIV gp 120 protein
  • The following was chosen along with the sequence

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>sp|P04578|ENV_HV1H2 Envelope glycoprotein gp160 OS=Human immunodeficiency virus type 1 (isolate HXB2 group M subtype B) GN=env PE=1 SV=2 MRVKEKYQHLWRWGWRWGTMLLGMLMICSATEKLWVTVYYGVPVWKEATTTLFCASDAKA YDTEVHNVWATHACVPTDPNPQEVVLVNVTENFNMWKNDMVEQMHEDIISLWDQSLKPCV KLTPLCVSLKCTDLKNDTNTNSSSGRMIMEKGEIKNCSFNISTSIRGKVQKEYAFFYKLD IIPIDNDTTSYKLTSCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNNKTFNGTGPCT NVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSVNFTDNAKTIIVQLNTSVEINCTRPN NNTRKRIRIQRGPGRAFVTIGKIGNMRQAHCNISRAKWNNTLKQIASKLREQFGNNKTII FKQSSGGDPEIVTHSFNCGGEFFYCNSTQLFNSTWFNSTWSTEGSNNTEGSDTITLPCRI KQIINMWQKVGKAMYAPPISGQIRCSSNITGLLLTRDGGNSNNESEIFRPGGGDMRDNWR SELYKYKVVKIEPLGVAPTKAKRRVVQREKRAVGIGALFLGFLGAAGSTMGAASMTLTVQ ARQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAVERYLKDQQLLGIWGCSG KLICTTAVPWNASWSNKSLEQIWNHTTWMEWDREINNYTSLIHSLIEESQNQQEKNEQEL LELDKWASLWNWFNITNWLWYIKLFIMIVGGLVGLRIVFAVLSIVNRVRQGYSPLSFQTH LPTPRGPDRPEGIEEEGGERDRDRSIRLVNGSLALIWDDLRSLCLFSYHRLRDLLLIVTR IVELLGRRGWEALKYWWNLLQYWSQELKNSAVSLLNATAIAVAEGTDRVIEVVQGACRAI RHIPRRIRQGLERILL

Chapter 4

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Chapter 5

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  • With that open reading frame, it was compared to the one that was found using the Uniprot

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Overall, they are both similar and the only difference that was significant was only due to the number of base pairs that were compared to.

Chapter 6

  • The ProtoParam tool was first used on the gp120 protein to attain information

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  • The parameters where then re-entered to allow the protein to be digested
  • The ProtScale was then used to look fore transmembrane segmenting

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  • The InterProScan was then used to find the right site of the domain

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  • The sequence was then used on the CD server in order to find the domain

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BIOL398-01: Bioinformatics Lab

  • Lab Journal
Kristoffer Chin: Week 2 Kristoffer Chin: Week 6 Kristoffer Chin: Week 11
Kristoffer Chin: Week 3 Kristoffer Chin: Week 7 Kristoffer Chin: Week 12
Kristoffer Chin: Week 4 Kristoffer Chin: Week 8 Kristoffer Chin: Week 13
Kristoffer Chin: Week 5 Kristoffer Chin: Week 9 Kristoffer Chin: Week 14


  • Shared Journal
BIOL398-01/S10:Class Journal Week 2 BIOL398-01/S10:Class Journal Week 6 BIOL398-01/S10:Class Journal Week 11
BIOL398-01/S10:Class Journal Week 3 BIOL398-01/S10:Class Journal Week 7 BIOL398-01/S10:Class Journal Week 12
BIOL398-01/S10:Class Journal Week 4 BIOL398-01/S10:Class Journal Week 8 BIOL398-01/S10:Class Journal Week 13
BIOL398-01/S10:Class Journal Week 5 BIOL398-01/S10:Class Journal Week 9 BIOL398-01/S10:Class Journal Week 14


  • Assignments
BIOL398-01/S10:Week 2 BIOL398-01/S10:Week 6 BIOL398-01/S10:Week 11
BIOL398-01/S10:Week 3 BIOL398-01/S10:Week 7 BIOL398-01/S10:Week 12
BIOL398-01/S10:Week 4 BIOL398-01/S10:Week 8 BIOL398-01/S10:Week 13
BIOL398-01/S10:Week 5 BIOL398-01/S10:Week 9 BIOL398-01/S10:Week 14

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