User: Sishuo Wang
Sishuo Wang • 190
- Reputation:
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- The Chinese University of Hong Kong
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- Google Scholar Page
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- Joined:
- 6 years, 10 months ago
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Posts by Sishuo Wang
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... in perl
$seq =~ /CAGGCATGCC ([ATGC]{3})+ TCATCGCTGG/x
print $1
...
written 1 day ago by
Sishuo Wang • 190
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... Would the following link help?
[https://david.ncifcrf.gov/conversion.jsp][1]
[1]: https://david.ncifcrf.gov/conversion.jsp ...
written 19 days ago by
Sishuo Wang • 190
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... Try this example command given by the book
> result_handle = NCBIWWW.qblast("blastn", "nt", "8332116")
It gave me the result within three minutes. ...
written 10 weeks ago by
Sishuo Wang • 190
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... Maybe [trimseq][1]?
[1]: http://emboss.sourceforge.net/apps/cvs/emboss/apps/trimseq.html ...
written 6 months ago by
Sishuo Wang • 190
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... Apologizes for confusion. I meant that they used two reference gene sets: euk and protist. I am not sure whether this was mentioned in your post. Sorry if I misunderstood your questions. Anyway, you can consider comparing your results with theirs using the same reference data set and maybe your resu ...
written 6 months ago by
Sishuo Wang • 190
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... It seemed to me that what you need is only a reference genome in the format of gbk (and of high quality particularly if there are /gene and /EC_number) so that the naming would be consistent. ...
written 6 months ago by
Sishuo Wang • 190
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... Hi Qingtian,
I guess it may be related to the reference gene set you were using. You might want to have a look at [Johnson et al., 2018][1] where the authors used BUSCO too but with different reference gene sets to evaluate protists' genome completeness.
[1]: https://academic.oup.com/gigascienc ...
written 7 months ago by
Sishuo Wang • 190
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... yes, seems weird to me. [González-Pech, et al., 2018][1] also talks about it, but 3.92e-84 and 1e-38 differ a lot. Any ideas?
[1]: https://academic.oup.com/bioinformatics/article/35/15/2697/5239655 ...
written 7 months ago by
Sishuo Wang • 190
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Comment:
C: Extract genes from gbk file.
... hi,
you may want to try [this one][1]
[1]: http://www2.warwick.ac.uk/fac/sci/moac/people/students/peter_cock/python/genbank2fasta/ ...
written 8 months ago by
Sishuo Wang • 190
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... hi shicheng, i think both [raxml][1] and [iq-tree][2] can work with binary data.
[1]: https://cme.h-its.org/exelixis/web/software/raxml/hands_on.html
[2]: http://www.iqtree.org/doc/Tutorial ...
written 8 months ago by
Sishuo Wang • 190
Latest awards to Sishuo Wang
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20 months ago,
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voted at least 25 times.
Popular Question
5.6 years ago,
created a question with more than 1,000 views.
For Which software can be used to visualize phylogenetic trees with a large number of OTUs (e.g. 50,000)
Student
6.0 years ago,
asked a question with at least 3 up-votes.
For Which software can be used to visualize phylogenetic trees with a large number of OTUs (e.g. 50,000)
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