Kristoffer Chin: Week 8

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



>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

 * For this task, the entry information found in http://www.expasy.org/sprot/ is to be given on the gp120 that was chosen.

Chapter 5

 * Using http://www.ncbi.nlm.nih.gov/gorf/gorf.html I took Subject 2 Visit 1 clone 1 from the previous HIV project that was in the Biology workbench to find its open reading frame.


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



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


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


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


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