Alternative software for gene and functional annotation and prediction

I'm looking for alternative software for gene and functional prediction, metabolic pathway construction and etc., is anyone willing to share their experience in yeast gene and functional prediction?

06 July 2012 8,721 2 View

Any nice gene and functional annotation software recommend by user experience?

There is too many sources of annotation software. Some can publish the complete genome even just using fully automatic annotation software. Yet, there is mis functional annotation. Different...

04 May 2012 8,642 0 View

I face a technical problem on newbler GUI.

I cannot make newbler run GUI after installation and restart, can anyone can help me solve such an issue? I'm using CentOS 6.2 and Redhat 6. Both have the same problem >_

04 May 2012 3,747 0 View

Other than velvet, abyss, newbler, CABOG and amos - can anyone recommend a good open source software?

Looking for user experience feedback

04 May 2012 6,767 8 View

Anyone mine to share advance analysis of assembly ?

After quality filter, assembly, and validation. Is there is anything else or tiny thing that user could missing up. I'm wandering, the exact definition for advance assembly analysis

04 May 2012 8,677 2 View

How solve such problem when convert newbler ace or std ace format file to amos bank format ?

During the conversion, the msg indicate the conversion fail, it's lock and lib not found. This situation also happend when I convert yeast velvet amos compatible to bank format.

04 May 2012 9,927 0 View

Any visualization software that shows pair end read information?

Do you know of any software that allows prediction and analyses of mis-assemble and QC of assembly result other than AMOS and CLC software?

04 May 2012 6,856 14 View

Is there any nice and recommended Gap Filling and gap extension software available?

I'm still newbie in NGS and my knowledge limited to few software. I'm trying to explorer to more software and method to gain my knowledge.

04 May 2012 8,323 0 View

Anyone know how to handle CABOG, assembler software. Can you explain how to run it ?

I failed to make it on either Illumina PE, Hiseq2000 (stuck at mery) and Roche 454 FLX (stuck to create overlap)

04 May 2012 443 7 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