User: Sishuo Wang

gravatar for Sishuo Wang
Sishuo Wang130
Reputation:
130
Status:
Trusted
Location:
The University of British Columbia
Scholar ID:
Google Scholar Page
Last seen:
4 hours ago
Joined:
4 years, 9 months ago
Email:
t**********@gmail.com

about me

Posts by Sishuo Wang

<prev • 38 results • page 1 of 4 • next >
0
votes
0
answers
90
views
0
answers
Comment: C: dN/dS analysis of genomes
... Maybe by setting mgene = in the control file? ...
written 7 days ago by Sishuo Wang130
1
vote
0
answers
90
views
0
answers
Comment: C: dN/dS analysis of genomes
... Hi Mehmet, I think calculating dn/ds per alignment is good. You can create quick trees for the alignment as input of codeml, otherwise you could let the programme do it. ...
written 7 days ago by Sishuo Wang130
0
votes
0
answers
91
views
0
answers
Comment: C: Protein binding domain database
... Hi yuabrahamliu, One way is to can try to collect all such domains, and search for them in databases like pfam, smart, etc. It might be time-consuming, though. ...
written 8 days ago by Sishuo Wang130
0
votes
2
answers
125
views
2
answers
Comment: C: How to know the mm9 genome size?
... Would [FetchChromSizes][1] be helpful? [1]: https://wiki.bits.vib.be/index.php/FetchChromSizes ...
written 8 days ago by Sishuo Wang130
0
votes
0
answers
117
views
0
answers
Comment: C: Positive selection analysis on gene family using the PAML package
... Hi, I think to focus on the specific clades/lineages you are interested in is good. [This paper][1] and [this one][2] may be helpful to have a look. Also, It seems to me that the distribution of all plant species might be too broad to do PAML positive selection analysis. [1]: https://academic. ...
written 26 days ago by Sishuo Wang130
0
votes
0
answers
164
views
0
answers
Comment: C: Swiss-Model vs. Modeller
... Both seem to me to be excellent tools, though you can always try [i-tasser][1] which has been in the 1st place in CASP for years. [1]: https://zhanglab.ccmb.med.umich.edu/I-TASSER/ ...
written 4 weeks ago by Sishuo Wang130
0
votes
1
answer
89
views
1
answers
Answer: A: How to download genes and corresponding pdb files?
... The following link may help you [link1][1], You can click on the tab "Sequences". [1]: https://www.rcsb.org/pdb/static.do?p=download/web_download/download.jsp ...
written 5 weeks ago by Sishuo Wang130
1
vote
1
answer
91
views
1
answers
Answer: A: Error Running codeml
... Hi ammarsabir15, In the second line of the control file, it is written as *treefile = tree.txt*. So, you may need to rename your tree file to "tree.txt" instead of "species.tree", and do the same thing for the alignment file ("seqfile.txt"). ...
written 5 weeks ago by Sishuo Wang130
0
votes
3
answers
1.7k
views
3
answers
Comment: C: how to find conserved region within a protein family for the construction of phy
... You can try [gblock][1] or [trimal][2]. Also, trees built using Maximum likelihood (available in MEGA5 I think) or Bayes methods instead of NJ might better reflect the evolutionary history of your sequences. [1]: http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=gblocks [2]: http://tr ...
written 5 weeks ago by Sishuo Wang130
0
votes
2
answers
110
views
2
answers
Comment: C: using NCBI SRA data for prinseq
... Exactly, it should perfectly work if you fix the problem of the line starting with the symbol "+". ...
written 5 weeks ago by Sishuo Wang130

Latest awards to Sishuo Wang

Supporter 2.6 years ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1984 users visited in the last hour