5

Comparing Biopython MetlingTemp to other calculators. I have written the recent version of MeltingTemp in Biopython's SeqUtils. I have extensively tested the Tm calculations against other programs like MELTING and Primer3Plus and other online Tm calculators with consistent results, thus I'm pretty confident that there is no gross error in the module. The ...


5

So, the problem is that you are probably using wrong class for your record. Compare Bio.SeqRecord class with Bio.GenBank.Record class. Reason why in your GenBank format you have this reference date (01-JAN-1980) is because your record has intrinsically no date attribute, so SeqRecord.format set undefined fields to default (look through the source code to see ...


3

My approach to this problem would be to use VMD (Visual Molecular Dynamics), where you can load multiple PDBs, perform structural and/or sequence alignment and analyse residue conservation within one program. VMD is a powerful molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in ...


3

This will be a complete answer, but it's got code, so it won't work as a comment. Working backwards from rtree(3), here's a way to build a phylo object from component parts, which might be helpful: children <- c(5, 1, 2, 3) parents <- c(4, 5, 5, 4) x <- matrix(c(parents, children), ncol = 2) tr <- list(edge = x, tip.label = 1:3, Nnode = 2) class(...


2

Incomplete sequences is a common problem. One way of getting around it is submitting your PDB ID list to an ID mapper. The one at Uniprot works well. Simply copy and paste your PDB ID codes. Make sure you're going from PDB to UniprotKB (see picture below. Hopefully you'll be able to map most if not all of your IDs. After you have that, download the text ...


2

@kmm's code works with a few tweaks. One problem your edgelist has is that it contains a singleton node, which ape does not like to deal with. Turning it into a proper phylo object means removing the singleton 'root' node and instead making the child of this singleton node the root. Here is an example using a slightly larger tree, which demonstrates how to ...


2

The Biopython 1.65 ABI parser should expose the chromatogram data, as of Biopython 1.66 it should expose everything. UPDATE: Example using this for plotting here: http://biopython.org/wiki/ABI_traces


2

I just received a PERL code snippet by the researcher behind sidirect2 which allows to calculate the Tm. I still do not know the source of the calculation discrepancy as the thermodynamics is beyond me. I post the code to conclude the question here. The can below can be saved into a .pl file and run from shell with the respective RNA sequence as a string ...


2

Using the SeqRecord object approach with Bio.SeqIO, you would do something like this: my_record.annotations["data_file_division"] = "PLN" my_record.annotations["date"] = "24-DEC-2015" Note that only valid NCBI GenBank divisions, or their EMBL equivalent, will be accepted.


1

You can use Ensembl (http://www.ensembl.org/index.html) to retrieve orthologues of the protein, and align them using one of many free, web based programs (such as ClusterOmega)


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