Kristoffer Chin: Week 8
Entry
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
- For this task, the entry information found in http://www.expasy.org/sprot/ is to be given on the gp120 that was chosen.
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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.
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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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