Check protein properties

[kimrutherford]

While working on #569 I noticed that the protein properties we show on the gene pages doesn't match the values in the PeptideStats.tsv file from PomBase V1.

There are many calculators on the web but they give quite different answers for some of the properties. So I'm not sure our values are OK.

As an example, for SPAC3G9.09c we have:

Isoelectric point    6.42
Charge at pH 7      -2.42

(Calculated using this Perl module: http://search.cpan.org/dist/BioPerl/Bio/Tools/pICalculator.pm )

This online calculator matches the values we have quite well (but not perfectly): http://protcalc.sourceforge.net/

Estimated pI = 6.46
Estimated charge at pH 7.00 = -2.4

This one gives somewhat different values: http://pepcalc.com/protein-calculator.php

Iso-electric point: pH 6.03
Net charge at pH 7: -3.5

This one: http://isoelectric.ovh.org/ gives the iso-electric point as: 5.83

[Antonialock]

Maybe it would be good to ask Steve (or someone else at biochemistry) which resource gives the best estimates? Some methods outperform other methods, but I don't know which one is regarded best/reliable.

[ValWood]

Ask pombelist which one people would prefer ?

[ValWood]

@Antonialock maybe you needed to provide the options?

[ValWood]

Also asked Steve's group

[Antonialock]

I wouldn’t know whether to suggest tools or pick algorithms recommended in papers.

Q: do general users even look at the number? Q2: would anyone who cares about the number go out themselves and find an estimate based on their favourite algorithm?

[ValWood]

Let's just pick one, (top google hit?)

[ValWood]

what are the options, we'll decide on the call

[Antonialock]

This paper compares different prediction methods: https://academic.oup.com/bioinformatics/article/32/6/821/1744386

They recommend an SVM based machine learning algorithm published here: https://www.ncbi.nlm.nih.gov/pubmed/22326964

[Antonialock]

Pride

[Antonialock]

https://www.ebi.ac.uk/pride/help/archive

[Antonialock]

https://web.expasy.org/compute_pi/

[ValWood]

document method used currently.

[mah11]

Documentation done. We decided that will do until & unless users clamor for something different.