Comments on: Survey of domain bubbles in protein sequence analysis

By: alexbateman

alexbateman — Tue, 27 Oct 2009 10:26:53 +0000

The Pfam domain graphics have changed with the new Pfam release 24.0. Graphics are now rendered on the client side. Because we have switched over to using HMMER3 there are now more partial hits to domains. An example protein is shown here:

http://pfam.sanger.ac.uk//protein/VAV_HUMAN

By: Visualization of internal repeats in proteins (or DNA) « Freelancing science

Thu, 24 Jan 2008 15:29:10 +0000

[...] complicated analysed sequence is, the more useful this approach seems to be, so for short proteins typical domain bubbles would work [...]

By: freesci

freesci — Mon, 01 Oct 2007 19:22:10 +0000

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

Pedro Beltrao — Mon, 01 Oct 2007 17:37:19 +0000

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

freesci — Tue, 25 Sep 2007 18:29:56 +0000

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

Akhilesh Pandey — Tue, 25 Sep 2007 16:45:20 +0000

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

max — Tue, 25 Sep 2007 16:16:40 +0000

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

nuin — Mon, 24 Sep 2007 19:28:00 +0000

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

Paulo