Can someone advise on using qiime?

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What will be best bacterial genome alignment tool for comparative analysis in terms of single nucleotide variation due to stress ?

Bioinformatic tool for genome variation comparision.

04 May 2018 974 1 View

Which is the primer designing tool recommended for gene expression studies?

Critical factors like codon, start codon, re site incorporation, etc have to be dealt with in making primers for gene expression studies, and hence: are there any recommended Softwares for the...

31 December 2013 8,096 13 View

Can anyone recommend a good vector for cloning a PCR amplified catabolic gene for protein expression studies?

I am trying to clone a catabolic gene amplified from metagenome via precise primer design.

09 October 2013 1,935 13 View

Track the difference

I have 2 bacterial genome sequences- i.e draft genomes. The genus are the same, but to discriminate on species level, what tools can I apply? There are a set of genes similar in both strains and...

11 December 2012 826 10 View

Has anyone used CopyControl Fosmid Library Production Kit? What are the product reviews?

I would want to use it for metagenomic library production.

08 September 2012 6,140 0 View

Anyone using Copy Control Bac cloning kit for metagenomic library construction?

Sludge metagenomic Library

08 September 2012 2,056 0 View

Is anyone dealing with Metagenomic library construction from sludge DNA ?

I am to begin one such task and have decided on Bac as my cloning vehicle, and restriction digestion as the next step using BamH1 and pst1.

04 May 2012 6,263 5 View

Does anyone know HRM channel in a 2 plex QIAGEN Rotor- Gene Q qPCR can be used as a separate channel?

I am going to have 3 different probes in my qPCR work that I am going to do. But I realized that the machine we have in the lab is a Rotor-Gene Q 2plex HRM Platform, saying it has green, yellow,...

01 March 2021 8,544 1 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

How can I retrieve FASTA sequence from gene ID or UID of a Gene ? I have GeneBank IDs ?

I treid to use Entrez Batch, but it redirects me to NCBI site. Is there any script of Linux or Python through which I can download Fasta sequence of list of gene ID ?

21 February 2021 7,783 12 View

Alternatives to traditional cloning of insert into backbone (dsDNA)?

Hi, I am stuck with a cloning experiment: The insert & backbone(bb) share one compatible end at 3' end(NotI) and one incompatible end at 5' end (XbaI for insert; HindIII for backbone). So i...

16 February 2021 1,664 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

What is the cause of a smear from direct DNA amplification from human buccal swab samples ?

Dear fellow scientists, I like to performed a direct amplification of a fragment of 222-bp DNA from human genome and use is for further analysis. By using the following methods, I obtained...

07 February 2021 891 3 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

Why cloning of gene into pCAMBIA1304 vector is unsuccessful?

I have tried to clone a specific gene into pCAMBIA1304 vector. But all the attempts failed. I used ligation kit from both Promega Corporation and Takara Bio. However, there was one time I used...

04 February 2021 525 1 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