User: Sishuo Wang

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Sishuo Wang190
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190
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The Chinese University of Hong Kong
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6 years, 10 months ago
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Posts by Sishuo Wang

<prev • 67 results • page 1 of 7 • next >
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Comment: C: Extract codon between two flanking sequences from FASTA
... in perl $seq =~ /CAGGCATGCC ([ATGC]{3})+ TCATCGCTGG/x print $1 ...
written 1 day ago by Sishuo Wang190
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Comment: C: Zebrafish Ensembl gene ID to RefSeq protein accession?
... 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 Wang190
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Comment: C: (biopython) qblast taking half hour - one search?
... 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 Wang190
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Answer: A: how to remove N loci in a global alignment for all strains
... Maybe [trimseq][1]? [1]: http://emboss.sourceforge.net/apps/cvs/emboss/apps/trimseq.html ...
written 6 months ago by Sishuo Wang190
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Comment: C: Low BUSCO completeness value for protists
... 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 Wang190
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Comment: C: Convert nucleotide fasta of contigs to protein sequence genbank
... 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 Wang190
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Comment: C: Low BUSCO completeness value for protists
... 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 Wang190
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Comment: C: bugs of blast (not intuitively evalue cutoff)
... 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 Wang190
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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 Wang190
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Answer: A: Phylogenetic tree with 0,1 matrix as the input?
... 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 Wang190

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Voter 20 months ago, voted more than 100 times.
Supporter 4.7 years ago, voted at least 25 times.

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