How to generate Synthetic DNA barcode dataset?

Help appreciated!! We are having Empirical data sets of plant barcodes (matK, ITS and rbcL), and want to compare analytical methodology used for Empirical data sets with the Synthetic data...

08 September 2019 813 8 View

How to simulate/generate DNA sequences with reference to the Singletone Species?

I am having many singleton Species (species representing only one DNA sequence). These singletons lack resolution potential as they are single, when applied machine learning classifiers singletons...

08 September 2019 2,973 3 View

Which are most preferred Alignment-free tools for matK and ITS2?

I have NCBI GenBank mined DNA sequences belonging to matK and ITS2 regions. I would appreciate if anyone suggests alignment free tools to calculate K-mer frequencies OR Genetic distances in order...

08 September 2019 2,646 5 View

How to remove ambiguous DNA characters form mulit-sequence FASTA file?

I am having unaligned multiple sequence FASTA file (don't want to align) with ambiguous characters: RYWSMKHBVDNS I want to remove/delete those characters... 1) I tried with mEMBOSS Readme:...

11 December 2017 3,043 7 View

Dealing with Mined DNA sequence: HELP in Alignment & Analysis?

09 October 2017 3,224 6 View

How do you find the K-mer size of a nucleotide sequence?

The size of K-mers is between 1 and 8, for nucleotide sequence it is recommended from 4 to 7. The programs found were all in Python, Pearl, Linux or C language which are not userfriendly. Please...

02 March 2015 1,768 9 View

Can anyone suggest software, R code or perl code for determining monophyla, where input is given in tree format (Newick file)?

I am having thousands of samples (DNA barcoded) for species confirmation (False positive or True positive species). This species confirmation is to be done on distance based and tree based...

07 August 2014 8,937 7 View

Can anyone assist with a query regarding R package, SPIDER (SPecies IDentity and Evolution)?

I am using R package, "SPIDER" (SPecies IDentity and Evolution), I got its tutorial, which describes analysis for: anoteropsis, dolomedes and sarkar files (input file .rda). The tutorial works...

07 August 2014 3,381 6 View

DNA barcoding, querry regarding tree based (cluster) methods for species identification?

I am working on success rate of DNA barcoding in identification of species using distance and tree based methods. Regarding distance based method, I have used Adhoc and species identifier and...

06 July 2014 6,078 11 View

Where can we get best webcourse on Python for Biologist or Bioinformatics?

Where can we get best web-course beginning from basic Python programming and using Kernels till analyzing data with Machine learning algorithms. I think most of the Biologist don't need much to...

01 January 1970 9,456 5 View

error in running a model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

error in modelling model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MGL tools

20 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

i have some problem with chtMultiRegionSimpleFoam

--> FOAM FATAL ERROR: Maximum number of iterations exceeded From function Foam::scalar Foam::species::thermo::T(Foam::scalar, Foam::scalar, Foam::scalar, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar) const) const [with Thermo = Foam::hConstThermo >; Type = Foam::sensibleEnthalpy; Foam::scalar = double; Foam::species::thermo = Foam::species::thermo >, Foam::sensibleEnthalpy>] in file /home/ubuntu/OpenFOAM/OpenFOAM-4.1/src/thermophysicalModels/specie/lnInclude/thermoI.H at line 66. FOAM aborting #0 Foam::error::printStack(Foam::Ostream&) at ??:? #1 Foam::error::abort() at ??:? #2 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::calculate() at ??:? #3 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::correct() at ??:? #4 ? at ??:? #5 __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6" #6 ? at ??:?

24 March 2021 0 0 View