Hi, I am new to modeller software and please give me your advice on the followings. I modeled a protein by using the modeller software and obtained the templates for the target and in order to pick up suitable templates out of those, E-value is needed to consider.If E-value is lesser then the better the template according to their publication.But the E-values are in negative and do I have consider the value with the negetive or do I have to consider just the value?. I am confused with that.
and when selecting the templates do I have to consider both E-value and the sequence alignment between template and target because some of the templates are above 40% sequence identity and some of them are lesser than it?. and again when selecting a template based on the dendogram to generate the models based on it, do I have to consider both resolution and the sequence identity?
Thank you.
It's been years since I used modeller but isn't the basic premise that you don't work with a template that's at ~40%? You need around 60-70% for template based alignment to work well, no?
Have you looked to see what negative e-values could mean? If they're all in a narrow range and not too negative, it could be an indication that they're all good e-values. From what I see, these e-values are sourced from protein-BLAST, so negative e values are a computational artifact, not really anything of significance.
Thank you ram for the comment. tem1 0.12E-03 tem2 0.50E-02 tem3 0.86E-04 tem4 0.25E-02 tem5 0.33E-03 tem6 0.11E-02 tem7 0.96E-03 These are the E values that I obtained for the potential templates and the sequence identity of these are higher than 25% ( as according to the tutorial). They did not indicate what does E value means in anyplace that is why I asked. For their example in the modeller tutorial, some of the potential templates have negative values for the E-values and some have zero E-values.So they picked the zero E-values ( according to the modeller publication lesser the E value, better the template).So that means without considering the negativity I have to just consider the value right? According to the tutorial and the publication ,selection of the template is based on the 40% sequence identity.I am not sure about the 60-70% for template based alignment.
Please do not add answers unless you're answering the top level question. This belongs as a reply to my comment. Please see http://biostars.org/t/how-to posts to learn how to use the forum better. I've moved your post to a comment for now.
sorry about that Ram.I made a mistake.