[Biopython-dev] Fwd: [biopython] MeltingTemp completely rewritten and extended (#192)

[Peter Cock]

Sebastian, could you comment on or review this?

Thanks, Peter

---------- Forwarded message ----------
From: *Markus Piotrowski*
Date: Saturday, June 29, 2013
Subject: [biopython] MeltingTemp completely rewritten and extended (#192)
To: biopython/biopython <biopython at noreply.github.com>


More or less completely rewritten and largely extended.
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.
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You can merge this Pull Request by running

  git pull https://github.com/MarkusPiotrowski/biopython MeltingTemp

Or view, comment on, or merge it at:

  https://github.com/biopython/biopython/pull/192
Commit Summary

   - MeltingTemp completely rewritten and extended

File Changes

   - *M* Bio/SeqUtils/MeltingTemp.py<https://github.com/biopython/biopython/pull/192/files#diff-0>(1107)

Patch Links:

   - https://github.com/biopython/biopython/pull/192.patch
   - https://github.com/biopython/biopython/pull/192.diff