How does one interpret the output from a 'PGLS-Relationships' analysis in Compare 4.6b?

03 April 2015 3,286 0 View

For a PGLS analysis in Compare 4.6, can anyone propose sources of error or solutions for the following problems?

I am using Compare 4.6 software to perform PGLS on a large set of trait values using a known phylogeny (based on genetic distance; Taxa = 23, Traits = 110, phylogeny = 1). The problem is that when...

03 April 2015 845 1 View

RAPD PCR: does every sample require a technical replicate or will a subset suffice?

In the interests of conserving time and resources, I would like to avoid performing replicates on every single sample, unless this is absolutely necessary. I have read in the literature that 5-10%...

07 August 2014 6,800 4 View

What statistical methods can be used to determine reproducibility between more than two groups of replicate samples?

I am analysing data obtained from experiments conducted on a group of 10 individuals in triplicate. In each replicate, the number of data points are not necessarily the same for each of the...

11 December 2013 2,693 4 View

Can you re-position a DNA ladder in a gel picture (you plan to publish) using image editing methods?

I am thinking about publishing work based on RAPD PCR. The problem I am having is that my gel pictures consist of several different experiments/primers (represented by 10 samples each) beside a...

07 August 2013 5,266 5 View

Can anyone provide an example of an input file for the program DfDist (Beaumont, 2008)?

The program detects loci influenced by selection by comparing their Fst values to a neutral simulation.

08 September 2012 3,055 2 View

In what format should AFLP data be submitted to software used for detecting selection?

I am aware that the detection is based on Fst values. However, should these be obtained using another program and then be transferred to DfDist, Bayescan etc. or should AFLP binary data be used...

08 September 2012 3,245 0 View

In preliminary screening of AFLP primer combinations to determine pairs which give optimal results, how many individuals should be screened?

Is this randomly decided by the researcher or is there a general principle they can base their decision on? I have read many papers looking for an answer but have yet to find an explanation on...

07 August 2012 3,348 7 View

What would be an adequate sample number for preliminary screening of AFLP primer pairs?

I want to make an accurate determination of the best primer pairs to use in a full-scale analysis but I don't want to use any more time or resources than I need to on a preliminary screening. I...

07 August 2012 1,838 3 View

What is the difference between genotype and haplotype data in the ped format?

Hi everybody In the ped format for genotype, alleles of any SNP are represented by two columns (one for each allele, separated by a space). Is a column sufficient for the haplotype to...

27 February 2021 1,965 1 View

Are there any databases for gene co-expression or expression pattern clustering?

I am currently working on gene clustering based on co-expression pattern in mouse brain. The problem is I do not have some solid way to test my result. Are there any suggestions for databases...

22 February 2021 4,374 3 View

Useful architecture for bioinformatics?

Hi Dear researchers In ensemble-based architectural design Which algorithms are more useful for classification? What is the difference between parallel and ensemble architecture? Thanks I am...

08 February 2021 2,727 5 View

Electron density difference maps(Fo-Fc): what is the meaning of negative densities (red blobs)?

Dear community, As far as I understand, negative density features point at stuff that is in the model, but not supported by experimental data. However, in many cases (e.g. attached image), when...

06 February 2021 2,847 2 View

Qiime2- No reads passed the filter. How to set the trunc value?

Hi, I am working on some 16S sequencing data, and seems some of them are low quality. I am not sure how to set the trunc value in dada2. qiime dada2 denoise-paired \ --i-demultiplexed-seqs...

30 January 2021 6,213 3 View

Which software to use to statistically analyze Telomere Length_TRF_Southern Blot?

I am trying to measure telomere length in an ant species using the TRF method, which is a Southern blot technique. Currently, I am struggling with analyzing the images and would appreciate any...

29 January 2021 604 3 View

MHC Rabbit Genome Annotation? Domain annotation of each MHC Rabbit Gene?

I want to find a database(s) or a method where I can find and bulk download all the rabbit MHC genes and domain annotation. In humans using Ensembl, all MHC genes have names and domains but in...

28 January 2021 7,722 2 View

Best tool to build missing residues, minimize and validate a ligand model?

I am working on a ligand that is co-crystalized to parotein, but the ligand is missing some residues that makes it appear as if it was separated into two ligands! what I need is to connect them...

23 January 2021 3,975 7 View

What's the role of bioinformatics in poultry science?

bioinformatics has a big importance in human science and lots are seeking to study that field, so it attracts me to know it's relation with poultry science and how we can benefit from it in...

20 January 2021 6,963 3 View

How can I get the chromosomal location of a list of genes?

I'm looking for a bioinformatics website to get the chromosomal location of a radish gene id list, but in one shot instead of doing it gene by gene. Is there a way to do this? Thanks

17 January 2021 8,810 3 View