User: manaswwm

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manaswwm40
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16 hours ago
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1 year, 3 months ago
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Posts by manaswwm

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Question regarding journal publications
... 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 manaswwm40
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Comment: C: sequence similarity analysis between groups of closely related DNA sequences
... 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 manaswwm40
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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 manaswwm40
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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 manaswwm40
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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 manaswwm40
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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 manaswwm40
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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 manaswwm40
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Comment: C: Combine two molecules and perform docking
... 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 manaswwm40
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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 manaswwm40
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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 manaswwm40

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)

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