User: gearoid

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gearoid200
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Posts by gearoid

<prev • 16 results • page 1 of 2 • next >
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Answer: A: BLOSUM80 values differ - but what's the reason?
... It looks like the two versions are using different units. In the first matrix the unit is 1/3 bit, while in the second matrix, it's 1/2 bit. From the second matrix: a scale of ln(2)/2.0 is the conversion factor for 'nats' to half bit units. ...
written 3.4 years ago by gearoid200
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Comment: C: [ Mustang ] Problem with Server
... Have you tried other inputs? You could just check if it produces an alignment of two chains only, it shouldn't take too long. I can't see anything wrong with your parameters or anything. If MUSTANG produces an alignment for a different set of files, then it could just be that it's crashing on the o ...
written 3.4 years ago by gearoid200
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Comment: C: [ Mustang ] Problem with Server
... Is there a file called 'core' in the directory where you ran MUSTANG? I find that it crashes on some inputs after the pairwise alignments, but before producing any output. ...
written 3.4 years ago by gearoid200
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Answer: A: Error when running clustal omega with python/biopython
... Closing the input file after writing to it, but before calling Clustal Omega, makes this work for me. Just add handle.close() after the call to SeqIO.write(). I think the way it is now, maybe the sequences aren't being written to that file until the script terminates (after the call to Clust ...
written 3.4 years ago by gearoid200
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Comment: C: Multiple sequence alignment
... I think it works as long as the file that you're writing to doesn't exist already, but you're right, it's sloppy--I updated my answer. The long string of parameters is why I didn't recommend MAFFT for this question, I was just trying to keep it simple. It's a great option, though. ...
written 3.4 years ago by gearoid200
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Comment: C: Locating a sequence in multiple fasta files
... I just tried this out, but although the python module installs just fine, I'm getting "command not found" when I try and run the script. Maybe it's getting copied to somewhere that isn't in my path (or not getting copied anywhere)? OK, when I try it without the --user flag, it works, so I reckon it ...
written 3.4 years ago by gearoid200
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Comment: C: Multiple sequence alignment
... Can you elaborate on why it's dangerous? I guess you can only run that command once, is that what you mean? I like MAFFT, but in this case I would probably want to use MAFFT L-INS-i or G-INS-i, rather than the default MAFFT parameters, and I just tried to give the simplest option I could think of ( ...
written 3.4 years ago by gearoid200
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Answer: A: Multiple sequence alignment
... If you have 120 FASTA files with one sequence each, and another with your wild type (and you're using Linux/OS X), first use cat to concatenate all the sequences into one file, e.g. cat seq1.fasta seq2.fasta ... seqN.fasta > all_my_sequences.fa or cat *.fasta > all_my_sequences.fa ...
written 3.4 years ago by gearoid200
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Comment: C: How to edit .PDB files fast ?
... As far as I know, the PDB file format defines the fields based on specific columns rather than whitespace. So previous fields in the atom record aren't guaranteed to be separated by whitespace. So this command will seem like it's working, but silently fail to extract certain atoms from the chain you ...
written 3.4 years ago by gearoid200
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Answer: A: How to edit .PDB files fast ?
... """ Extract a single chain from a PDB file """ from __future__ import print_function import Bio.PDB import Bio.PDB.PDBIO import sys import argparse class ChainSelect(Bio.PDB.Select): def __init__(self, target_chain): self.target_chain = ...
written 3.4 years ago by gearoid200

Latest awards to gearoid

Scholar 3.4 years ago, created an answer that has been accepted. For A: How to create empty Biopython MultipleSeqAlignment object?
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: How to edit .PDB files fast ?
Scholar 3.4 years ago, created an answer that has been accepted. For A: How to create empty Biopython MultipleSeqAlignment object?
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: How to edit .PDB files fast ?
Supporter 3.4 years ago, voted at least 25 times.
Scholar 3.5 years ago, created an answer that has been accepted. For A: How to create empty Biopython MultipleSeqAlignment object?

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