Chris Rhodes Week 8: Difference between revisions
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RSVNFTDNAKTIIVQLNTSVEINCTRPNNNTRKRIRIQRGPGRAFVTIGKIGNMRQAHCNISRAKWNNTLKQIASKLRE | RSVNFTDNAKTIIVQLNTSVEINCTRPNNNTRKRIRIQRGPGRAFVTIGKIGNMRQAHCNISRAKWNNTLKQIASKLRE | ||
QFGNNKTIIFKQSSGGDPEIVTHSFNCGGEFFYCNSTQLFN | QFGNNKTIIFKQSSGGDPEIVTHSFNCGGEFFYCNSTQLFN | ||
*From the list of gp160 proteins found when searching for gp120 in the first step 5 sequences were chosen to be used in the mass retrieval exercise. The UniProt ID numbers of the 5 sequences are P04578, P03377, P03375, P35961, and P05877. From the options for downloading the sequences I chose the FASTA format, this combined sequence FASTA file can be found [[Media:CHR_Fasta1_20111019.fasta | here] | *From the list of gp160 proteins found when searching for gp120 in the first step 5 sequences were chosen to be used in the mass retrieval exercise. The UniProt ID numbers of the 5 sequences are P04578, P03377, P03375, P35961, and P05877. From the options for downloading the sequences I chose the FASTA format, this combined sequence FASTA file can be found [[Media:CHR_Fasta1_20111019.fasta | here]] | ||
==HIV Structure Project== | ==HIV Structure Project== | ||
Revision as of 15:08, 19 October 2011
For today's lab we will working out of the Bioinformatics for Dummies 2nd edition book performing selected activities from Chapters 2, 4, 5, and 6 but modifying the protocols to apply to the current website formats and the use of HIV-1 gp120.
In Class Activities
Retrieving Protein Sequences
- The protein retrieved in this exercise is HIV-1 gp120. It was found by going to ExPASy and searching "HIV gp120 envelope protein" using the UniProtKB database, but verified independent gp120 protein could not be found. The gp120 protein sequence was instead taken from an entry of gp160 which contains the gp120 sqeuence. The UniProtKB entry of the gp160 protein used is found hereand the sequence of the gp120 protein, shown as the highlighted residues within the gp160 protein sequence, is found here http://www.uniprot.org/blast/?about=P04578[33-511] -> This address couldn't be properly hyperlinked due to the [33-511] text causing problems with the linking format.
- The fasta form of the gp120 protein sequence was retrieved from the entry page and is shown here:
>sp|P04578|33-511 KLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVVLVNVTENFNMWKNDMVEQMHEDIISL WDQSLKPCVKLTPLCVSLKCTDLKNDTNTNSSSGRMIMEKGEIKNCSFNISTSIRGKVQKEYAFFYKLDIIPIDNDTTSY KLTSCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVI RSVNFTDNAKTIIVQLNTSVEINCTRPNNNTRKRIRIQRGPGRAFVTIGKIGNMRQAHCNISRAKWNNTLKQIASKLRE QFGNNKTIIFKQSSGGDPEIVTHSFNCGGEFFYCNSTQLFN
- From the list of gp160 proteins found when searching for gp120 in the first step 5 sequences were chosen to be used in the mass retrieval exercise. The UniProt ID numbers of the 5 sequences are P04578, P03377, P03375, P35961, and P05877. From the options for downloading the sequences I chose the FASTA format, this combined sequence FASTA file can be found here
HIV Structure Project
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