Comments on: Survey of domain bubbles in protein sequence analysis http://freelancingscience.com/2007/09/24/survey-of-domain-bubbles-in-protein-sequence-analysis/ visualization, protein science, open science and freelancing science Sat, 04 Jul 2009 05:16:54 +0000 http://wordpress.com/ hourly 1 By: Visualization of internal repeats in proteins (or DNA) « Freelancing science http://freelancingscience.com/2007/09/24/survey-of-domain-bubbles-in-protein-sequence-analysis/#comment-277 Visualization of internal repeats in proteins (or DNA) « Freelancing science Thu, 24 Jan 2008 15:29:10 +0000 http://freesci.wordpress.com/2007/09/24/survey-of-domain-bubbles-in-protein-sequence-analysis/#comment-277 [...] complicated analysed sequence is, the more useful this approach seems to be, so for short proteins typical domain bubbles would work [...] [...] complicated analysed sequence is, the more useful this approach seems to be, so for short proteins typical domain bubbles would work [...]

]]> By: freesci http://freelancingscience.com/2007/09/24/survey-of-domain-bubbles-in-protein-sequence-analysis/#comment-41 freesci Mon, 01 Oct 2007 19:22:10 +0000 http://freesci.wordpress.com/2007/09/24/survey-of-domain-bubbles-in-protein-sequence-analysis/#comment-41 You're right Pedro - they do not look that much different. I focused here on the differences, but in fact there was not that much to write about. While I don't use SMART that much because of its sensitivity, I was using its scripts for my own servers for some time :). You’re right Pedro – they do not look that much different. I focused here on the differences, but in fact there was not that much to write about.

While I don’t use SMART that much because of its sensitivity, I was using its scripts for my own servers for some time :) .

]]> By: Pedro Beltrao http://freelancingscience.com/2007/09/24/survey-of-domain-bubbles-in-protein-sequence-analysis/#comment-40 Pedro Beltrao Mon, 01 Oct 2007 17:37:19 +0000 http://freesci.wordpress.com/2007/09/24/survey-of-domain-bubbles-in-protein-sequence-analysis/#comment-40 I am in EMBL so I am biased but I like SMART. You picked a protein that apparently does not have any hits with SMART so it is showing the PFAM hits. The SMART hits look a bit nicer :). Still, I guess your point is that there has been very little change in how we represent protein domain information on a picture. I am in EMBL so I am biased but I like SMART. You picked a protein that apparently does not have any hits with SMART so it is showing the PFAM hits. The SMART hits look a bit nicer :) . Still, I guess your point is that there has been very little change in how we represent protein domain information on a picture.

]]> By: freesci http://freelancingscience.com/2007/09/24/survey-of-domain-bubbles-in-protein-sequence-analysis/#comment-37 freesci Tue, 25 Sep 2007 18:29:56 +0000 http://freesci.wordpress.com/2007/09/24/survey-of-domain-bubbles-in-protein-sequence-analysis/#comment-37 Hi Paulo, unfortunately annotation of DNA sequences is not my area of expertise. Hopefully the suggestion of Max will work for you. Hi Akhilesh, I completely forgot about other than general annotation servers (forgive me, I work in bacterial subsystems). The graphics of HPRD entries looks pretty neat - I liked for example a difference between phosphorylation and dephosphorylation. I hope to include it in a second part of this survey. Hi Paulo, unfortunately annotation of DNA sequences is not my area of expertise. Hopefully the suggestion of Max will work for you.

Hi Akhilesh, I completely forgot about other than general annotation servers (forgive me, I work in bacterial subsystems). The graphics of HPRD entries looks pretty neat – I liked for example a difference between phosphorylation and dephosphorylation. I hope to include it in a second part of this survey.

]]> By: Akhilesh Pandey http://freelancingscience.com/2007/09/24/survey-of-domain-bubbles-in-protein-sequence-analysis/#comment-36 Akhilesh Pandey Tue, 25 Sep 2007 16:45:20 +0000 http://freesci.wordpress.com/2007/09/24/survey-of-domain-bubbles-in-protein-sequence-analysis/#comment-36 Have you looked at Human Protein Reference Database. Try the link below for a representative entry: http://www.hprd.org/summary?protein=01819&isoform_id=01819_1&isoform_name=Isoform_2 Have you looked at Human Protein Reference Database. Try the link below for a representative entry:

http://www.hprd.org/summary?protein=01819&isoform_id=01819_1&isoform_name=Isoform_2

]]> By: max http://freelancingscience.com/2007/09/24/survey-of-domain-bubbles-in-protein-sequence-analysis/#comment-35 max Tue, 25 Sep 2007 16:16:40 +0000 http://freesci.wordpress.com/2007/09/24/survey-of-domain-bubbles-in-protein-sequence-analysis/#comment-35 Paulo, use the UCSC browser. add your annotation as a "custom track", export to pdf. you can add colors, links, etc. I found UCSC usually sufficient and you can re-work the pdf before submitting in something like illustrator... Paulo, use the UCSC browser. add your annotation as a “custom track”, export to pdf. you can add colors, links, etc. I found UCSC usually sufficient and you can re-work the pdf before submitting in something like illustrator…

]]> By: nuin http://freelancingscience.com/2007/09/24/survey-of-domain-bubbles-in-protein-sequence-analysis/#comment-34 nuin Mon, 24 Sep 2007 19:28:00 +0000 http://freesci.wordpress.com/2007/09/24/survey-of-domain-bubbles-in-protein-sequence-analysis/#comment-34 Hi Would you have any good ones for DNA sequences? I have some data that I need to generate good figures. Paulo Hi

Would you have any good ones for DNA sequences? I have some data that I need to generate good figures.

Paulo

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