How to analyse the miranda 3.3a output and to check cross species conservation status of predicted targets?

we have used miranda 3.3a for target prediction for our novel miRNA dataset obtained from NGS data. We have obtained the output. This is a very big file and difficult to analyze manually. Further...

04 May 2016 9,992 0 View

We have obtained many novel miRNAs for human from NGS data. Which computational method be used for target prediction?

As some popular ones like targetscan demand miRNA ids, means it can not be used for novel ones. Further as the number of miRNAs is quite high (nearly 400), we need a software capable of handling...

03 April 2016 1,267 8 View

What happens to miRNA* if it doesn't get degraded in cytoplasm?

The bio-genesis of miRNA as explained by many researchers explain that miRNA duplex gets separated in single strands after entering cytoplasm. miRNA enters into RISC while miRNA* gets degraded....

05 June 2014 6,707 9 View

Can you suggest some tools for classification of miRNA families on the basis of putative function?

Though the exact function of many miRNA is unknown or not experimentally validated. But target prediction is there for all. So on the basis of common targets, maybe we can group and derive some...

04 May 2014 7,902 17 View

How can I trim the terminal oligonucleotide from EST sequences of a large datasets? (nearly 60,000 sequences to be trimmed)

I am working on an EST data assembly and annotation project. After screening with VecScreen no significant matches were detected. As a cautious step, we plan to trim the terminal 25-30 nt length...

04 May 2014 9,701 3 View

Can anyone help with cleaning of EST sequences?

I have started working on EST data processing of cotton. As a first step, we have screened all the deposited EST sequences by 'VecScreen' to detect vector sequence contamination. But in all the...

04 May 2014 5,562 3 View

How to calculate PIC, MI and H' values for ISSR primers?

We are working with SSR and ISSR primers. The resolving power of various SSR primers to distinguish among the genotypes could be evaluated by calculating PIC, Marker index, Shanon index. We used...

31 December 2013 5,972 8 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