Adarsh Singh

9 Questions 8 Answers 0 Followers

Questions related from Adarsh Singh

How to speed -up RAxML process?

I am trying to build a tree using 5003 aligned sequences having an alignment length of 261. I have tried to use threads as suggested in RAxML guide but its been 2 days already and still running,...

12 October 2020 7,879 2 View

How to extract mapped reads for paired-end reads?

I am working with paired-end reads, and want to extract all those reads which map to an assembly. Since its a paired-end reads, I am confused if I should extract reads for which both (forward and...

23 August 2020 4,265 3 View

How to use Pfam HMM files?

I need HMM files of 43 marker genes specified for CPRs in order to estimate their completeness and contamination using checkm. I first tried TIGRfam database and found only 41 of them, so I tried...

30 July 2020 1,500 0 View

How to do MD simulation after doing docking with Autodock?

I am trying to find an inhibitor for a protein, and for that purpose, I did preliminary docking using Autodock to find potential inhibitors. Now, I need to check if that docking is stable or not....

11 May 2020 9,922 3 View

How to get drug structure (pdb) from .xml file available on drugbank?

I am working with molecular docking and I want to dock the whole database of human approved drugs over my protein, but for that, I will need PDB file of those drugs. I looked it up over drugbank...

28 April 2020 4,941 2 View

How to plot rarefaction curve for whole-genome shotgun sequencing?

I am trying to assemble the whole genome of a metagenome-assembled genome. For this purpose, I am trying to plot a rarefaction curve which will tell me if I need to do any deep sequencing so that...

11 March 2020 9,725 3 View

How to build a new HMMs from a database (say NCBI)?

I am new to HMMs and was thinking to build new HMMs based on the NCBI database(which is available to download) or SILVA, so that it can be used by some other program. Can you suggest any tool...

05 February 2020 6,331 1 View

How to combine two illumina reads?

I am working on WGS, and I have generated two pairs-end reads (total 4, two forward, and 2 reverse)(the difference is in their DNA purification method). Now, I want to combine these two pairs of...

28 November 2019 4,022 4 View

How to find binding/affinity energy of protein-ligand interaction, and also visualize it?

I am working on beta-lactamases and trying to find in-silico binding/affinity energy of beta-lactam antibiotics with the protein. I tried using Autodock-vina, but the order I am getting seems to...

05 November 2019 4,008 1 View