What is the formula to calculate the critical value of correlation?

I am calculating the correlation values between two data sets of size 257. I want to know what is the critical value of correlation for a sample size of 257. I tried searching on the web, but...

11 December 2013 9,131 18 View

What is the minimum coverage and how to identity percentage for protein domains?

I am trying to find out existence of protein domains in a set of sequences. I am using BLASTX for the task. I have made a BLASTX of my sequences with the ProDom sequences. I used an e-value cutoff...

10 November 2013 4,606 3 View

How to get consensus at ambiguous sites?

I have a set of aligned sequences in fasta format. I want to get consensus out of the alignment. In case of most of the sites one of the base is showing maximum occurrence. In case of sites where...

09 October 2013 3,770 2 View

Ambiguity with bacterial ITS regions?

ITS regions are used for identifications of bacterial species. But while observing bacterial genomes it is seen that tRNA sequences are present in the ITS regions present between 16S rRNA and 23S...

09 October 2013 4,033 5 View

How to screen genomes for compositional studies?

I am working with around 2600+ genomes and wish to study the genome, gene and intergenic features among various groups. In case of taxonomical groups which have very few representatives, there is...

08 September 2013 9,505 6 View

Isn't a prokaryotic gene continuous?

I work on E. coli genomes and while going through the various genes present, I have seen (link) that in the coordinates area of the description it is suggested to join different regions of genome....

07 August 2013 9,078 7 View

Is there any free online access to a good system for researchers?

I am working at genomes level and I have a shortage of computational resources to do the tasks I want to. So could you please suggest where I can get free online access to a good system for my...

07 August 2013 9,192 5 View

How do I Rectify NCBI C++ Exception? ncbi::CMemoryFileSegment::CMemoryFileSegment()

I have tried running a command line blast. The query file is a multi fasta file containing 2600 sequences. It was made a BLASTX against a proteins sequences (ProDom) of size 2 GB (prodom.phr :...

07 August 2013 369 0 View

Should regulatory sequences be included in intergenic sequences?

I am working on finding the functional signatures/remains of regulatory regions, RNAs and proteins in the intergenic sequences (IGs) of E. coli K12 MG1655. I have a few doubts regarding the...

07 August 2013 1,811 1 View

How efficient are PERL and PHP in designing bioinformatics tools? What are the pros and cons of each and which is most commonly used and why?

Out of my experience I think the basic difference among both of them lies in speed and usage. PHP can be used for creating online tools. PERL can also be used, but PHP is more easy to handle to...

06 July 2013 428 4 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