Joe Healey
  • Member for 4 years, 7 months
  • Last seen more than a month ago
what is the difference between local identity and global identity for homolog finding?
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3 votes

If you want a purely alignment based approach to begin to infer homology (note I say infer, as we stated in the comments, this isn't sufficient to say 2 sequences are homologs), I would use a Multiple ...

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Importing GFF file with Biopython
2 votes

I would use BCBio for gff handling as it is written to directly interface with BioPython’s object model. The only downside is that I believe it is no longer actively supported. It is however the ...

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A tool or webserver for building PSSM matrix
2 votes

If you take a look at my answer in this BioStars post, you can generate a PSSM using AlignIO in Biopython:

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How to find the sum of all sequences in a multifasta file
2 votes

Here’s a function that I keep around for calculating the individual lengths of fasta sequences falens(){ awk '/^>/ {if (seqlen){print seqlen}; print ;seqlen=0;next; } { seqlen += length($0)}END{...

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How to determine a protein's cellular location based on its sequence?
2 votes

You can run the sequence through tools like SignalP to look for cell surface signals and so on, which will give you a clue about where I is bound for. None of these tools will give you an absolutely ...

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Profile of conservation between bacterial sequences and human protein
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2 votes

I'm not sure what you mean by it being a mess? That looks like a pretty good alignment to me, and it most certainly has aligned all the sequences. You are nearly always going to have gaps (see my MSA ...

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How do I generate a color-coded tanglegram?
2 votes

As an alternative (though I realise this doesn't really answer the OPs question directly), Dendroscope and Treemap can also produce these types of plots. I don't know if they'll do coloured ...

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Phyre2 vs ITasser, completely different models generated
1 votes

This may not be the whole answer to the question, but one key difference between Phyre and ITasser (I think I'm correct in saying), is that Phyre only returns regions of the model it considers to be ...

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Mutations in sequences relative to reference (histogram)
1 votes

In answer to the comments, you can do multiple pair wise alignments and then concatenate them to visualise, if MSA is not the way to go. I have a script you can find here which will draw a graph of ...

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Calculating the charge of a peptide computationally
1 votes

I've used PropKa in the past to get isoelectric points. Pretty simple to use: https://github.com/jensengroup/propka-3.1

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How does blastn sort output?
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1 votes

Edit I stand corrected. @Daniel Standage correctly pointed out that the below is only true for a single query, or for the sorting of hits within those found by a given query. Otherwise they're sorted ...

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