Zrusso Biol 368 week 8
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Bioinformatics for Dummies Work
- This website is completely different from what the book shows so I'm not sure if I'm getting the right thing
- [1]
>sp|P04578|33-511 KLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVVLVNVTEN FNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVSLKCTDLKNDTNTNSSSGRMIMEKG EIKNCSFNISTSIRGKVQKEYAFFYKLDIIPIDNDTTSYKLTSCNTSVITQACPKVSFEP IPIHYCAPAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVI RSVNFTDNAKTIIVQLNTSVEINCTRPNNNTRKRIRIQRGPGRAFVTIGKIGNMRQAHCN ISRAKWNNTLKQIASKLREQFGNNKTIIFKQSSGGDPEIVTHSFNCGGEFFYCNSTQLFN STWFNSTWSTEGSNNTEGSDTITLPCRIKQIINMWQKVGKAMYAPPISGQIRCSSNITGL LLTRDGGNSNNESEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKAKRRVVQREKR
- downloaded 5 sequences of gp160 in FASTA format to my comp. I guess I'll have to hand edit it to just get gp120?
- Media:Gp120_on_swissprot_zrusso.png
- Media:Entry_info_on_gp160_zrusso.png
- under 'enzyme and pathway databases' there is a link called REACT_6185 that takes me to a ridiculous diagram of boxes and lines that describe the entire system of enzymatic activities dealing with humans, one of which is HIV infection. not that helpful or comprehensible.
- I cannot find a comments section describing the things they talk about, maybe due to the fact that gp160 is not an enzyme and is simply part of a complex, not independent
- Found it, its called 'general annotation' now and simply lists its function, subunit structure and location on the HIV virion itself. Also talks about domain, post-transcription modifications, sequence similiarities as well as miscellaneous info.
- the cross references show links to sequence databases, 3D structure databases, and family and domain databases
- gp120 itself is listed under Pfam, SUPFAM, and Gene3D
- features has been renamed 'sequence annotation'
- Includes sections molecule processing, regions, sites, amino acid modifications, natural variations, experimental info and a color coded diagram showing secondary structure
- I like that i can click on any word (almost) and get its definition in the context of Bioinformatics
- So the SwissProt page didn't seem to have the DNA sequence itself, just the protein sequence so I had to go to EMBL to get what i 'think' is the correct DNA sequence
- Media:ORF finder on gp160 zrusso.png
