http://biovis.net/forum/discussions/feed.rss Sat, 18 May 13 06:55:35 -0800 All Discussions - BioVis Forum en-CA http://biovis.net/forum/discussion/90/the-importance-of-distance Tue, 16 Apr 2013 19:31:38 -0800 mercicle 90@/forum/discussions This regards the "communication" of residues and the "8 Angstrom" cutoff. We need to better understand if this is a hard rule and whether the quantitative relationships of residues that are further than 8 Angstrom matters or not (or if there is some linear or other functional relationship in the effect of one residue on another (as a function of distance)).
Thanks!]]> http://biovis.net/forum/discussion/66/tim-data-question Mon, 18 Mar 2013 11:50:07 -0800 mercicle 66@/forum/discussions We were wondering what the process was for selecting the TIM set (other than scTIM/dTIM) that you provided. Did you do a search for homologous sequences of scTIM and only accept based on an E-value threshold? Any other parameters and alignment algorithm specifications that you used?
Thanks,
John]]> http://biovis.net/forum/discussion/54/functional-prediction Sun, 03 Mar 2013 11:46:32 -0900 mercicle 54@/forum/discussions http://www.ebi.ac.uk/Tools/services/web/blastresult.ebi?jobId=ncbiblast-I20130303-203656-0339-20931910-pg&tool=ncbiblast&context=protein&analysis=ffdp-query
under the "functional prediction" tab.]]> http://biovis.net/forum/discussion/46/user-scenario Wed, 13 Feb 2013 10:22:36 -0900 mercicle 46@/forum/discussions When you are studying sequences, how many do you compare at a time for example in a MSA? So in terms of the distribution of your time, what % would you allocate to:
2 at a time
3-10
10-20
...

This is just an example categorization. You can estimate the more accurate one...
Thanks!
John]]> http://biovis.net/forum/discussion/43/the-response-to-the-model Wed, 06 Feb 2013 04:05:26 -0900 mercicle 43@/forum/discussions http://biovis.net/forum/discussion/47/papers Thu, 14 Feb 2013 16:55:50 -0900 mercicle 47@/forum/discussions http://biovis.net/forum/discussion/45/ordering-of-amino-acids Thu, 07 Feb 2013 05:24:09 -0900 mercicle 45@/forum/discussions http://biovis.net/forum/discussion/44/httpwww.mathmed.orgraydatatim_sequences_fasta.txt Wed, 06 Feb 2013 14:34:31 -0900 mercicle 44@/forum/discussions 2 instances of A2BLD3_HYPBU
2 instances of Q7LZE5_MELGA
2 instances of E4NNF4_HALBP
2 instances of TPIS_METLZ
...]]> http://biovis.net/forum/discussion/24/what-do-you-want-to-see-from-a-large-multiple-sequence-alignment-msa-datasets Wed, 24 Oct 2012 23:52:16 -0800 khoanguyen 24@/forum/discussions
I saw several posters on visualizing large MSA data set. I have knowledge in visualization and I have some ideas of visualizing large MSA (in my visualization point of view). However, in order to make the visualization useful, I would like to ask for the kind of features that biologist want to see in a large MSA. For instance, would you want to see mis-alignments or the transition of amino acid between sequences?

Bests,
KN]]>