How to perform R^2 and p-value in Pcoa Plot?

Dear All, I have the weighted and unweighted distance matrix output file from QIIME2. I would like to find the Community structure differed significantly between the groups according to the beta...

08 September 2019 3,016 3 View

How to import biom format obtained from QIIME2 into Tax4Fun?

Hi All, Ive tried to run tax4fun using biom file obtained from qiime2 platform. Ive attached my text file coverted from biom format. How do I rectify this error?...

06 July 2019 1,014 1 View

Clarification on Proteome Discoverer Output file?

We have done LC/MS-MS analysis and executed Proteome Discoverer for identification of proteins. In the output, I found there are many proteins fragments and also found that one protein present...

10 November 2018 4,299 5 View

How to find significantly expressed proteins from proteome discoverer ??

Dear all, i am a new baby in the field of proteomic. Now I have the multiconcencous results obtained from proteome discoverer. I need to find the significantly expressed proteins between three...

05 June 2018 3,250 2 View

How to assign Taxonomic Classification for OTU tables?

I am new to metagenomics. I downloaded a 16s rRNA data from sra and generated OTU table using USEARCH. How to assign Taxonomic classification to OTU table. I tried with the following...

01 February 2018 2,957 2 View

What is the exact workflow of finding alternative splicing through RNA Seq

I am working on identifying tissue specific alternative splicing event in plants e.g rice. I have done till mapping to the reference genome. I am stuck to continue from the mapping results.

07 August 2017 3,587 1 View

What is skipped exon annotations file?

07 August 2017 7,829 1 View

How to convert .maegz format to PDB format ?

I have a docking results of one protein and one ligand in .maegz format. I need to visualise this result in discovery studio visualiser. But DS visualizer doesn't support .maegz format. So how to...

02 March 2017 6,190 6 View

How to get the complete graph after extened the nanoseconds from 10-20?

I have extended the simulation from 10ns to 20ns using .cpt file during molecular dynamics run,when i am trying to analyze the result i am getting the graph only from 10ns to 20ns instead of...

01 February 2017 2,464 3 View

Is there any idea for creating a perl module

I have assigned to create a small Perl module which can be using for bioinformatics and bio statistics. I have searched for many ideas. But almost all ideas are already there in CPAN. Can anyone...

09 October 2016 7,499 4 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

Mixed ANOVA with some normal and some non-normal data?

I am looking to run a 2x5 Mixed ANOVA to examine Sensory Processing Sensitivity in Highly Sensitive People (HSP) and Non_HSP. My Between-Subjects factor is HSP and Non-HSP. All participants tested...

11 February 2021 1,445 6 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

Why sometimes current- voltage plot in chemiresistors/ FET does not pass through the origin?

I am trying to measure resistance from I-V curve from a chemiresistor/ FET sensor with a keithly sourcemeter. The substrate is soaked/ wet with protein and phosphate buffer only. But the I-V line...

24 January 2021 8,009 3 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