Moderator: Joe

gravatar for Joe
Joe16k
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Location:
United Kingdom
Website:
http://www2.warwick.ac...
Twitter:
JRJHealey
Last seen:
2 hours ago
Joined:
4 years, 5 months ago
Email:
j*********@gmail.com

Recently finished my PhD, so now I pretend to know what I’m talking about on Bioinformatics forums...

Posts by Joe

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Comment: C: How to blastn a very short query sequence? Identifying telomeres in assembly
... Do you actually need alignment for this, or are the matches (reasonably) well conserved? Fuzzy matching, as already mentioned, or a regex approach might be sufficient? ...
written 2 hours ago by Joe16k
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Comment: C: How to find positions in the alignments at which the target sequence is not iden
... You are moving the goalposts now, getting the indexes of all the different positions is the output you requested, so that's the code I wrote. If you need a specific form of output, you need to be explicit about this in your question. You also haven't shown what you've tried on this front. You can ...
written 2 hours ago by Joe16k
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Comment: C: Question regarding journal publications
... I think you're underestimating the role of the thesis in the UK PhD process. Every UK PhD absolutely is judged on their making of a contribution to science, but to suggest papers are the only way to do that isn't accurate in my view. ...
written 3 hours ago by Joe16k
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Comment: C: How to find positions in the alignments at which the target sequence is not iden
... That should be easy enough. I'd suggest unrolling the list comprehension in to a proper loop structure, and then you just add a few `if` statements to ensure the character in question is not `X` or `-`. You could edit the list comp, but it starts to get unwieldy after a while. Off the top of my hea ...
written 4 hours ago by Joe16k
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Comment: C: How to find positions in the alignments at which the target sequence is not iden
... What do you want to do if the consensus has an ambiguous character? Otherwise you just need to loop over the sequences in the alignment: from Bio import AlignIO from Bio.Align import AlignInfo # To generate a trivial 'dumb' consensus aln = AlignIO.read(file, format) summary = Alig ...
written 7 hours ago by Joe16k
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Comment: C: how to download FASTA formated sequences from SCOPe
... 2 things: 1. If your question fits in a single sentence, you almost certainly have not provided enough information. What you've already tried and how/why it didn't work is a good start. 2. This is not a `Forum` type post, so I've changed it, but please bear in mind for the future. ...
written 16 hours ago by Joe16k
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Comment: C: Question regarding journal publications
... Yep - its a very backwards system. Your analogy is not quite right, as the expectation is not that the researcher themselves pay. It is most certainly a con that we have to pay to publish and pay to access oftentimes. ...
written 16 hours ago by Joe16k
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Comment: C: Question regarding journal publications
... I'd add to this that in the UK, its actually pretty unusual to get papers during the PhD as they're only about 3 years long, particularly in experimental biology. It's a bit more normal in chemistry and physics. It's certainly something academics will push for, as long as it adds to, and not distrac ...
written 16 hours ago by Joe16k
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Comment: C: Question regarding journal publications
... Welcome to the broken world of academic publishing. For the record, there are lots of journals that support open-access science (not that this always means you don't have to pay, just that you don't pay to access). Typically, you're going to be looking at online journals since they aren't passing ...
written 17 hours ago by Joe16k
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Comment: C: How to find positions in the alignments at which the target sequence is not iden
... Those numbers should correspond to the indexes you are interested in, exactly what is the problem? If you want to generalise this for the full alignment you can do: from Bio import AlignIO aln = AlignIO.parse(..., ...) for i in range(aln.get_alignment_length()): if len(se ...
written 1 day ago by Joe16k

Latest awards to Joe

Appreciated 16 hours ago, created a post with more than 5 votes. For C: is fortran still used in bioinformatics?
Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Run a Python program in Ubuntu
Popular Question 10 days ago, created a question with more than 1,000 views. For Merging gff/gbk to create a 'full' gbk
Popular Question 13 days ago, created a question with more than 1,000 views. For Merging gff/gbk to create a 'full' gbk
Scholar 4 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Scholar 5 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Run a Python program in Ubuntu
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: fasta seq header
Scholar 6 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Scholar 7 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Run a Python program in Ubuntu
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Merging gff/gbk to create a 'full' gbk
Appreciated 11 weeks ago, created a post with more than 5 votes. For C: is fortran still used in bioinformatics?
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Merging gff/gbk to create a 'full' gbk
Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: cuda-accelerated sequence alignment program
Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: fasta seq header
Good Answer 12 weeks ago, created an answer that was upvoted at least 5 times. For A: How to split a multi fasta file into individual chromosomes
Appreciated 12 weeks ago, created a post with more than 5 votes. For C: is fortran still used in bioinformatics?
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: biopython string object
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Run a Python program in Ubuntu
Scholar 3 months ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: fasta seq header
Scholar 3 months ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Scholar 3 months ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: fasta seq header

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