User: manaswwm
manaswwm • 40
- Reputation:
- 40
- Status:
- New User
- Location:
- Last seen:
- 16 hours ago
- Joined:
- 1 year, 3 months ago
- Email:
- m*******@gmail.com
Posts by manaswwm
<prev
• 21 results •
page 1 of 3 •
next >
0
votes
4
answers
168
views
4
answers
... I think journals have converted themselves into brands these days, the more well-known a brand is, more you pay for publishing. The ones who don't charge money are typically not so well recognized (read : negligible impact factor). If you are okay with that then they (low impact factor journals) are ...
written 16 hours ago by
manaswwm • 40
0
votes
3
answers
128
views
3
answers
... Have you tried different metrics with which you can comment on the degree of variance in between different groups of sequences? For example : pairwise nucleotide differences in between a group and among different groups? Or, maybe have a "consensus" sequence for each "group" and then check its pairw ...
written 10 days ago by
manaswwm • 40
0
votes
0
answers
79
views
0
answers
Comment:
C: pathway related to specified gene
... Not sure if this would help : I tried doing something similar using Cytoscape, I had a "node" of interest and I was able to extract associated interactions of that node from various different datasets (so a network which is formed by extracting information associated with my "node" of interest from ...
written 16 days ago by
manaswwm • 40
0
votes
0
answers
74
views
0
answers
Comment:
C: energy minimization calculation
... Have you tried the following things:
-Write a short email to the admins of this service asking them about this problem? I have never used this service however to me it seems that the service is restricted to certain users.
-tried using other simulation suites (Gromacs, which is free to use) for en ...
written 16 days ago by
manaswwm • 40
0
votes
0
answers
105
views
0
answers
Comment:
C: Fatal Error in Gromacs
... What this error means is there is no HA3 entry in the residual topology (.rtp) file for GLY residue in OPLS FF (Force Field). I would suggest you to see the the .rtp file of OPLS FF and search what is the naming scheme there along with charge and rename your HA3 accordingly (as long as you know what ...
written 17 days ago by
manaswwm • 40
0
votes
1
answer
92
views
1
answers
Answer:
A: About Energy Minimization
... When I first started using gromacs I found it really useful to follow Bevan's lab tutorials - http://www.mdtutorials.com/gmx/index.html. Maybe you will find them helpful too. ...
written 20 days ago by
manaswwm • 40
0
votes
0
answers
113
views
0
answers
Comment:
C: How can I parse GFF3 using BCBio?
... Is it possible for you to share a short snapshot of your gff file? ...
written 21 days ago by
manaswwm • 40
0
votes
0
answers
65
views
0
answers
... Just out of curiosity, if I take Augmentin as an example - I think it could be possible to form a possible structure of Augmentin by docking amoxicillin with clavulanic acid? Although this will not be as straightforward as smallmolecule-protein docking and not as reliable either, but this could be a ...
written 21 days ago by
manaswwm • 40
0
votes
0
answers
113
views
0
answers
Comment:
C: How can I parse GFF3 using BCBio?
... The tutorial (https://pythonhosted.org/gffutils/) is very straightforward, for example let us presume that the local database that you have created is by the name **db** and the gene whose CDS you would like to extract is assigned name **gene**, then you can accomplish what you want to by the follow ...
written 4 weeks ago by
manaswwm • 40
0
votes
0
answers
113
views
0
answers
Comment:
C: How can I parse GFF3 using BCBio?
... Try this package in python - https://pythonhosted.org/gffutils/
This package creates a "local" database from your gff file that you can interact with in relatively easier manner. For instance, I was able to extract start stop position of gene along with exons coding for that gene and their start an ...
written 4 weeks ago by
manaswwm • 40
Latest awards to manaswwm
Teacher
11 months ago,
created an answer with at least 3 up-votes.
For C: network visualization (multiple data source integration)
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1056 users visited in the last hour