Zrusso Biol 368 week 8: Difference between revisions
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*This website is completely different from what the book shows so I'm not sure if I'm getting the right thing | *This website is completely different from what the book shows so I'm not sure if I'm getting the right thing | ||
*[http://www.uniprot.org/uniprot/P03377 gp120 UniProt page] | |||
>sp|P04578|33-511 | >sp|P04578|33-511 | ||
KLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVVLVNVTEN | KLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVVLVNVTEN | ||
| Line 19: | Line 20: | ||
*the cross references show links to sequence databases, 3D structure databases, and family and domain databases | *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 | **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]] | |||
**reading frames +1 and -2 are the best matches to my DNA sequence | |||
*Did it again, except using the protein sequence I retrieved off of SwissProt instead of the accession number and it worked | |||
**[[Media:Run_2_ORF_finder_gp160_zrusso.png]] | |||
**Then again, when looking at the ORF's it found, it has little 'x' under all the sequences and it kept trying to find DNA bases, not recognizing the peptides so I don't think it worked | |||
*went to expasy.com and then went to resources and under 'p' was ProtParam | |||
**input my sequence of gp120 and got [[Media:ExPASy_ProtParam_results_zrusso.txt]] | |||
*Used ProtScale and the Kyte/Doolittle scale with a window size of 19 | |||
**[[Media:Pscale15138.gif]] image from this, it says that a number over 1.6 is good but nothing is over 1.1. their method of lowering a piece of paper until you no longer see sharp peaks only gets me maybe two peaks and they aren't even that sharp | |||
*used Eisenburg scale and it is lower, which it is supposed to be I believe, it is still just like the previous one where I may have 2 peaks but thats it and those aren't even that definitive | |||
*Trying TMHMM, and I just get two straight lines across the graphic, one at 1 and a thicker one at 1.2 and they are pink indicating they are outside all the time | |||
**[[Media:TMHMM_model_zrusso.png]] | |||
**It should be like this because gp120 is entirely outside the virus | |||
*using PROSITE to scan for post transcription modifications to gp120 | |||
**No surprise it found a lot of glycosylation sites | |||
**it also found a lot of phosphorylation sites and myristoylation(?) sites | |||
**[[Media:PROSITE_of_gp120_zrusso.png]] | |||
*Now on to finding the domains of gp120 | |||
**First is InterProScan | |||
***[[Media:InterProScan_results_zrusso.png]] | |||
***it finds it as gp120! | |||
***our research showed that gp120 itself is split into two domains, and all these results just show it as one it seems | |||
**Next is CD Domain | |||
***again sees it as a gp210 superfamily which is good | |||
***this one even shows a sequence alignment between the search query and its domains | |||
***again no mention of it being two domains | |||
***[[Media:CD_Domain_results_zrusso.png]] | |||
**Last chance with Motif Scan | |||
***checked all of their databases to see if it could find the two domain gp120 | |||
***Same results as the other two, it exists but does not mention the two domains | |||
==HIV Structure Research Project== | |||
*Bobby, Alex and I were thinking of still focusing on the difference in individuals before and after the onset of AIDS, but this time we will be using the V3 region DNA to determine if there is a change in structure (and therefore perhaps function) of the V3 region before and after progression to AIDS | |||
*We would be using the V3 sequences from the rapid progressor group pre- and post-CD4 levels hitting 200 and comparing that to patients who did not develop AIDS while V3 region DNA was available and see if there are any similarities to either pre- or post-CD4 levels hitting 200 | |||
*we hypothesize that there will be a change in structure of V3 region leading up to onset of AIDS, but after AIDS sets in and the immune system crashes there will be a reduction in conformational changes in V3 | |||
{{zrusso Biol 368}} | {{zrusso Biol 368}} | ||
Latest revision as of 23:12, 25 October 2011
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
- gp120 UniProt page
>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
- reading frames +1 and -2 are the best matches to my DNA sequence
- Did it again, except using the protein sequence I retrieved off of SwissProt instead of the accession number and it worked
- Media:Run_2_ORF_finder_gp160_zrusso.png
- Then again, when looking at the ORF's it found, it has little 'x' under all the sequences and it kept trying to find DNA bases, not recognizing the peptides so I don't think it worked
- went to expasy.com and then went to resources and under 'p' was ProtParam
- input my sequence of gp120 and got Media:ExPASy_ProtParam_results_zrusso.txt
- Used ProtScale and the Kyte/Doolittle scale with a window size of 19
- Media:Pscale15138.gif image from this, it says that a number over 1.6 is good but nothing is over 1.1. their method of lowering a piece of paper until you no longer see sharp peaks only gets me maybe two peaks and they aren't even that sharp
- used Eisenburg scale and it is lower, which it is supposed to be I believe, it is still just like the previous one where I may have 2 peaks but thats it and those aren't even that definitive
- Trying TMHMM, and I just get two straight lines across the graphic, one at 1 and a thicker one at 1.2 and they are pink indicating they are outside all the time
- Media:TMHMM_model_zrusso.png
- It should be like this because gp120 is entirely outside the virus
- using PROSITE to scan for post transcription modifications to gp120
- No surprise it found a lot of glycosylation sites
- it also found a lot of phosphorylation sites and myristoylation(?) sites
- Media:PROSITE_of_gp120_zrusso.png
- Now on to finding the domains of gp120
- First is InterProScan
- Media:InterProScan_results_zrusso.png
- it finds it as gp120!
- our research showed that gp120 itself is split into two domains, and all these results just show it as one it seems
- Next is CD Domain
- again sees it as a gp210 superfamily which is good
- this one even shows a sequence alignment between the search query and its domains
- again no mention of it being two domains
- Media:CD_Domain_results_zrusso.png
- Last chance with Motif Scan
- checked all of their databases to see if it could find the two domain gp120
- Same results as the other two, it exists but does not mention the two domains
- First is InterProScan
HIV Structure Research Project
- Bobby, Alex and I were thinking of still focusing on the difference in individuals before and after the onset of AIDS, but this time we will be using the V3 region DNA to determine if there is a change in structure (and therefore perhaps function) of the V3 region before and after progression to AIDS
- We would be using the V3 sequences from the rapid progressor group pre- and post-CD4 levels hitting 200 and comparing that to patients who did not develop AIDS while V3 region DNA was available and see if there are any similarities to either pre- or post-CD4 levels hitting 200
- we hypothesize that there will be a change in structure of V3 region leading up to onset of AIDS, but after AIDS sets in and the immune system crashes there will be a reduction in conformational changes in V3
