User: Sishuo Wang

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Sishuo Wang140
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Posts by Sishuo Wang

<prev • 48 results • page 1 of 5 • next >
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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 14 days 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 4 weeks 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 10 weeks 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 11 weeks 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 3 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 3 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 3 months ago by Sishuo Wang140
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Comment: C: dN/dS analysis of genomes
... I think that should work. ...
written 3 months ago by Sishuo Wang140
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Comment: C: Find all sequence of a specific genus amplified by a couple of primers
... Hi Shred, Maybe you can try the tools introduced by [this paper][1]. You can find the scripts in the supplemental files. [1]: https://academic.oup.com/gbe/article/7/12/3416/2467318 ...
written 3 months ago by Sishuo Wang140
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Comment: C: dN/dS analysis of genomes
... Hi Mehmet, Sorry, not sure. Have you got anything in the mlc file? Or was the analysis disrupted? By the way, there was a typo in "eqfile = all.paml". ...
written 3 months ago by Sishuo Wang140

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