User: yamule

gravatar for yamule
yamule180
Reputation:
180
Status:
Trusted
Location:
Japan
Website:
https://github.com/yamule
Last seen:
3 days, 4 hours ago
Joined:
1 year, 4 months ago
Email:
k***************@gmail.com

Hobbyist.

Working for a commercial company but this & github account are managed for private purpose.

Posts by yamule

<prev • 51 results • page 1 of 6 • next >
0
votes
0
answers
143
views
0
answers
Comment: C: Best way to identify proteins within a family?
... I think checking boot strap values of phylogenetic trees and checking conservation of important residues in alignments are essential for such a detail analysis. (There are some automatic approach such as orthomcl (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC403725/) but as I haven't tried this soft ...
written 26 days ago by yamule180
0
votes
0
answers
143
views
0
answers
Comment: C: Best way to identify proteins within a family?
... the sentence " In my case, my proteins don't have a specific domain characterizing them, and share a common domain with the rest of the family (e.g. the 7TM domain). " is confusing. You are going to find a "subfamily"? Btw, I think you have to draw phylogenetic trees in that case. ...
written 27 days ago by yamule180
0
votes
0
answers
196
views
0
answers
Comment: C: Finding pairwise alignment between two multifasta files for similarity search
... I googled the errormessage "Alignment score and position are not consensus." and thought that is caused by overflow of variable. One or some of your sequences might be too long for that module. https://github.com/10XGenomics/cellranger/blob/master/tenkit/lib/python/striped_smith_waterman/ssw.c ...
written 8 weeks ago by yamule180
0
votes
0
answers
174
views
0
answers
Comment: C: Phi/Psi torsion angles replication
... :thinking_face_emoticon: I have no idea then. Try superposition (select N-terminal 5 or 10 residues & A->align in PyMol) and check where discrepancy starts (ribbon mode or line mode will work). ...
written 3 months ago by yamule180
0
votes
0
answers
174
views
0
answers
Comment: C: Phi/Psi torsion angles replication
... How are you doing about omega? [https://en.wikipedia.org/wiki/Dihedral_angle#Proteins][1] [1]: https://en.wikipedia.org/wiki/Dihedral_angle#Proteins ...
written 3 months ago by yamule180
0
votes
0
answers
183
views
0
answers
Comment: C: NCBI bacterial Morphology, environment and temperate data
... I use bioproject xml for such purpose. ftp://ftp.ncbi.nlm.nih.gov/bioproject/ you need plenty of RAM to parse xml, though. ...
written 3 months ago by yamule180
0
votes
2
answers
372
views
2
answers
Comment: C: Expression Network vs PPI Network
... No. I have used intact https://www.ebi.ac.uk/intact/downloads , but it is not tissue specific, I think. ...
written 4 months ago by yamule180
1
vote
1
answer
306
views
1
answers
Comment: C: Problem with PDB, DSSP and Protein solvent accessibility
... I think it is written in the paper. (This one [http://proceedings.mlr.press/v32/zhou14.html][1] ? I'm not sure cuz I haven't read it.) There are many papers about Secondary Structure or Solvent Accessibility prediction. https://scholar.google.co.jp/scholar?as_ylo=2005&q=secondary+structure+pre ...
written 4 months ago by yamule180
0
votes
2
answers
372
views
2
answers
Answer: A: Expression Network vs PPI Network
... > If I use basal brain tissue gene expression to construct a network, > compared to using PPI from STRING, will one provide more relevant info > than the other? I know that a gene will encode for a specific protein > but just because geneA is highly correlated with geneB, doesn't > ne ...
written 4 months ago by yamule180
1
vote
1
answer
306
views
1
answers
Answer: A: Problem with PDB, DSSP and Protein solvent accessibility
... DSSP is this http://swift.cmbi.ru.nl/gv/dssp/ DSSP can calculate secondary structure and solvent accessibility of (residues in) protein using pdb formatted file as input. Please read the introduction. http://www.princeton.edu/~jzthree/datasets/ICML2014/cullpdb.tar.gz has over 8000 pdb files in it, ...
written 4 months ago by yamule180

Latest awards to yamule

Autobiographer 8 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 13 months ago, created an answer that has been accepted. For A: Reason of excluding homolog protein in protein subcellular location prediction

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1364 users visited in the last hour