User: SimonCB765

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SimonCB765150
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Posts by SimonCB765

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Mapping Drug/Chemical Names To Cas Number
... The question is which mapping you trust more/has greater coverage. Do you trust UniProt to record the NCBI IDs more accurately and completely, or NCBI to record the UniProt accession more accurately and completely. The way I did it was to go from all my sources to UniProt. In the case of NCBI gene I ...
written 6.1 years ago by SimonCB765150
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Comment: C: Mapping Drug/Chemical Names To Cas Number
... Unfortunately, I never found anything that did that. I ended up using UniProt accessions as my 'true' ID, and mapped TTD target IDs and NCBI gene IDs to UniProt accessions (along with all other IDs I needed). Not perfect, but going between UniProt and NCBI gene IDs was relatively simple. ...
written 6.1 years ago by SimonCB765150
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Answer: A: Mapping Drug/Chemical Names To Cas Number
... If your drug is in the Therapeutic Target Database, then you can use their file of cross-references to get the CAS number (along with other identifiers). ...
written 6.1 years ago by SimonCB765150
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Answer: A: Extraction Of Certain Lines Which Starts And Ends With A Particular Description.
... My Perl's not brilliant, but the problem with your first approach is that you're only printing out the line when it has >> in it. What you want is to set a flag when you see that, and turn the flag off when you see Complete (similar to your second approach). I get the output you want on the sa ...
written 6.1 years ago by SimonCB765150
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Comment: C: Using Blast From Within Perl.
... If you installed the latest version did you install Blast or Blast+? They renamed the latest versions to Blast+ when they updated them a couple years ago. Secondly, you could take a look at the code for the PISCES redundancy removal scripts. They call Blast from within them, although they are quite ...
written 6.2 years ago by SimonCB765150
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Comment: C: No Such File Or Directory - Errno::Enoent - Error Only Occurs In Ubuntu - It Wor
... The new line issue can definitely cause a 'file does not exist error'. I've had that happen a few times when copying files from a Windows box to a Unix server. ...
written 6.2 years ago by SimonCB765150
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Answer: A: Counting Gaps In A Column Of Alignment
... My Perl/BioPerl is a bit rusty, but I'll take a stab at answering this. The warning seems pretty straightforward. If you check the docs for slice it says that "Sequences with no residues in the slice are excluded from the new alignment and a warning is printed", which I imagine explains the warnings ...
written 6.2 years ago by SimonCB765150
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Comment: C: Counting Gaps In A Column Of Alignment
... Do you mean that the gap counting itself is not working or the result is not being printed out? You don't appear to be printing out the gap count anywhere in your code, so if it's not being printed out I would imagine that's the problem. ...
written 6.2 years ago by SimonCB765150
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Comment: C: Calculating The Instability Index Using Protparam And Biopython
... Sorry, I forgot to say that I had attempted that as well. It still seems to give different answers. I do agree with you about the usefulness of the instability predictions though. At this stage it's probably more a sense of curiosity/completeness that's leading me to try and work this out. ...
written 7.6 years ago by SimonCB765150
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Calculating The Instability Index Using Protparam And Biopython
... Hi, I've been trying to use the BioPython Bio.SeqUtils.ProtParam module to perform bulk calculations of the instability index of proteins. The only problem with this approach is that the BioPython implementation doesn't allow the amino acid sequence to contain amino acid codes B, J, O, U, X and Z. ...
protein biopython written 7.6 years ago by SimonCB765150 • updated 7.6 years ago by Neilfws48k

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