User: Sishuo Wang

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Sishuo Wang140
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140
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The University of British Columbia
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22 hours ago
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5 years, 6 months ago
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Posts by Sishuo Wang

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Comment: C: How to extract intronic regions from a Genbank file?
... You may wish to try this one [gff2fasta][1] by specifying the feature (--feature; Line 499 in the Perl script). [1]: https://github.com/minillinim/gff2fasta ...
written 11 weeks ago by Sishuo Wang140
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Comment: C: Number of citations of an article per year using PMIDs
... Have a try of the pubmedy add-in in chrome and you will see the number of citations as ![enter image description here][1] [1]: https://www.novoprolabs.com/images/2017121915136672881056.png ...
written 5 months ago by Sishuo Wang140
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Comment: C: Removing columns coded by -,N or ? in Alignments
... You can have a look at [this][1]. Alternatively, you may wish to try [UGENE][2] for removing gaps. For other characters, it might be possible to convert them into '-' first? [1]: https://stackoverflow.com/questions/28220301/python-remove-special-column-from-multiple-sequence-alignment [2]: htt ...
written 5 months ago by Sishuo Wang140
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Comment: C: how to download all protein sequnces of a bacteria using ncbi ftp site?
... should be included in *.faa ...
written 6 months ago by Sishuo Wang140
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Comment: C: File format conversion to clustal using biopython
... Hi, I think [seqret][1] from EMBOSS can do the job. You can set the [output format][2] as clustal. [1]: https://www.ebi.ac.uk/Tools/sfc/emboss_seqret/ [2]: https://www.ebi.ac.uk/seqdb/confluence/display/THD/EMBOSS+seqret#EMBOSSseqret-sequence ...
written 7 months ago by Sishuo Wang140
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Comment: C: tools to align DNA sequences against protein sequence
... [exonerate][1] may be a good option. [1]: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate-user-guide ...
written 7 months ago by Sishuo Wang140
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Comment: C: OrthoMCL problem when connecting with mysql
... You can try [orthofinder][1] or [get_homologues][2] instead for gene family clustering or identification of orthologs. Neither of them needs mysql connection. [1]: https://github.com/davidemms/OrthoFinder [2]: http://aem.asm.org/content/79/24/7696.full ...
written 8 months ago by Sishuo Wang140
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Comment: C: Orthofinder: orthogroup graph
... It seems that the author of orthofinder does not suggest changing the inflation index. [link][1] [1]: https://github.com/davidemms/OrthoFinder/issues/34 ...
written 8 months ago by Sishuo Wang140
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Comment: A: How I can find flanking regions
... Hi, You may feel bedtools flank ([link][1]) helpful, [1]: http://bedtools.readthedocs.io/en/latest/content/tools/flank.html ...
written 8 months ago by Sishuo Wang140
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Comment: C: dN/dS analysis of genomes
... I think that should work. ...
written 8 months ago by Sishuo Wang140

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