[Biopython-dev] [Biopython - Feature #3432] (New) Updated/Extended module MeltingTemp in Bio.SeqUtils

[redmine at redmine.open-bio.org]

Issue #3432 has been reported by Markus Piotrowski.

----------------------------------------
Feature #3432: Updated/Extended module MeltingTemp in Bio.SeqUtils
https://redmine.open-bio.org/issues/3432

Author: Markus Piotrowski
Status: New
Priority: Normal
Assignee: 
Category: 
Target version: 
URL: 


Dear Biopython developers,

I updated/extended the MeltingTemp module of SeqUtils and would be happy if you would consider it for implementing. Please find the source code attached. Any feedback is appreciated.
'Old' module:
One method, Tm_staluc, which calculates the melting temperature by the nearest neighbor method, using two different thermodynamic data sets for DNA and RNA. Fixed salt correction formula.
'Updated' module:
1. Three different Tm calculations: one 'rule of thumb' (Tm_Wallace), one using approximative formulas basing on GC content (Tm_GC) and one using nearest neighbor calculations (Tm_NN).
2. The new Tm_NN allows the usage of different thermodynamic datasets (8 tables are included for Watson-Crick base-pairing) and includes tables for mismatches (including inosine) and dangling ends. The datasets are Python dictionaries; the user can use his own datasets or change/update existing tables for his needs.
3. Seven different formulas to correct for salt concentration, including correction for Mg2+ ions (method salt_correction).
4. Method chem_correction which allows for Tm correction when using DMSO and formaldehyde.

I haven't touched the old Tm_staluc method (except adding some comments [labelled 'MP'] and a deprecation warning). Actually, the method has two problems on the RNA side: The dataset for RNA is faulty and 'U' isn't considered as input. Of course this problems can easily be fixed, however, I would prefer (if it is decided to accept the updated module) to completely exchange the body of Tm_staluc for calls to Tm_NN (as outlined in the comments).

There is one thing, that I'm uneasy with: For terminal mismatches, I used thermodynamic data from a patent application that has been withdrawn (http://patentscope.wipo.int/search/en/WO2001094611). Actually, I found the reference in the manual for Primer3 which also seems to use these data (http://primer3.sourceforge.net/primer3_manual.htm). Indeed, the Primer3 source (which is distributed under GPLv2) contains the data.

Best wishes,

Markus


----------------------------------------
You have received this notification because this email was added to the New Issue Alert plugin


-- 
You have received this notification because you have either subscribed to it, or are involved in it.
To change your notification preferences, please click here and login: http://redmine.open-bio.org