Moderator: Joe

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Joe18k
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Trusted
Location:
United Kingdom
Website:
http://www2.warwick.ac...
Twitter:
JRJHealey
Last seen:
an hour ago
Joined:
5 years, 4 months ago
Email:
j*********@gmail.com

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

Currently a Research Fellow at the University of Warwick Medical School, and the CEO and Founder of biotech startup www.nanosyrinx.com

Posts by Joe

<prev • 3,205 results • page 1 of 321 • next >
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Comment: C: blastn with short sequences gives no results in the corresponding genome
... You might want to take a look specifically at PrimerBlast (https://www.ncbi.nlm.nih.gov/tools/primer-blast/) which is designed specifically for this. ...
written 2 hours ago by Joe18k
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Comment: C: run a tool from python
... You are right that you need `subprocess` to run the command. You can either express your full paths in the command, or use `os.chdir()` to move to new folders. If you're running a `perl` script from within `python` though, this strikes me as not the most efficient process. I'm going to leave the p ...
written 3 days ago by Joe18k
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Comment: C: mauve alignment results meaning
... Sorry for the silly question, but you actually ran the mauve/progressiveMauve algorithm after reading the sequences in to the software right? If so, then yes, that indicates little to no similarity as far as I can tell. If you are confident in the assembly process (though you haven't actually menti ...
written 4 days ago by Joe18k
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Comment: C: mauve alignment results meaning
... Is that an assembly? If memory serves, the red bars demarcate discontinuous boundaries between sequences. That looks like a LOT of contigs - is this normal for your organism? If not, are you sure your assemblies are good? ...
written 4 days ago by Joe18k
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Answer: A: Adding gene names to fasta file
... Here's a biopython solution: from Bio import SeqIO import sys with open(sys.argv[1], 'r') as fh: for name, record in zip((line for line in fh.readlines()), SeqIO.parse(sys.argv[2], 'fasta')): record.description = record.description.replace(record.id+' ', '') ...
written 5 days ago by Joe18k
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Comment: C: K-mer sequencing vs sequence-alignment
... >What would happen if we did match many k-mers but they were all scattered, i.e. one k-mer sequence here, and one k-mer sequence there In case it wasn't obvious in my answer, this is exactly what we **do** do already. Don't fall in to the trap of thinking kmer methods imply any kind of 'contigui ...
written 6 days ago by Joe18k
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Comment: C: K-mer sequencing vs sequence-alignment
... No idea about a definitive resource, but a cursory google turns up things like: https://datasciencehongkong.files.wordpress.com/2018/02/dna2vec.pdf https://academic.oup.com/gigascience/article/8/2/giy165/5266304 https://angus.readthedocs.io/en/2017/kmers-and-sourmash.html If you look up "kmer di ...
written 6 days ago by Joe18k
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Comment: C: False positives in homology
... This question needs far more detail in order to be answerable. For starters: how is this list of homologues produced? In what sense are you considering something a false positive? ...
written 6 days ago by Joe18k
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Comment: C: CD-HIT: representative sequence vs consensus sequence
... That would be my assumption, yep :) ...
written 6 days ago by Joe18k
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Comment: C: K-mer sequencing vs sequence-alignment
... I don't know/haven't read the paper, but my immediate guess would be that they are doing something as I described above. That is, they figure out the 'kmer library' from a sequence (or a subset thereof) and then look for these kmers within the query sequence. Because the k is small, you will expect ...
written 6 days ago by Joe18k

Latest awards to Joe

Scholar 5 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: Run a Python program in Ubuntu
Scholar 6 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: Run a Python program in Ubuntu
Popular Question 29 days ago, created a question with more than 1,000 views. For Merging gff/gbk to create a 'full' gbk
Scholar 6 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: fasta seq header
Commentator 12 weeks ago, created a comment with at least 3 up-votes. For C: fasta seq header
Appreciated 12 weeks ago, created a post with more than 5 votes. For A: what are the big questions in bioinformatics field nowadays
Popular Question 3 months ago, created a question with more than 1,000 views. For Merging gff/gbk to create a 'full' gbk
Scholar 3 months ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: fasta seq header
Scholar 4 months ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Things you wish you knew when entering the bioinformatics field
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Run a Python program in Ubuntu
Appreciated 4 months ago, created a post with more than 5 votes. For A: what are the big questions in bioinformatics field nowadays
Popular Question 4 months ago, created a question with more than 1,000 views. For Merging gff/gbk to create a 'full' gbk
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Run a Python program in Ubuntu
Scholar 4 months ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Scholar 4 months ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Scholar 5 months ago, created an answer that has been accepted. For A: Run a Python program in Ubuntu
Scholar 5 months ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: fasta seq header
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Run a Python program in Ubuntu
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: fasta seq header

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