After metagenomics analysis, which tool is suitable for accurate gene finding and comparison?

More Muhammad Abdul Ghafar's questions See All

Can we classify HV and LV lines based on line length?

I have dataset which shows the length of power lines. I need to classify the lines based on the line length. Is there a rule to classify the High voltage (HV) and low voltage (LV) lines based on...

03 March 2021 4,116 4 View

Why the results when using wall thickness and when using shell conduction are different in ansys fluent?

Actually, I am running cfd simulation for a heat exchanger which has two fluids one hot and other one is cold fluid. there is a solid domain between them, which I removed and instead I have used...

01 March 2021 9,537 2 View

How much pressure we can reduce at the outlet to avoid Reverse Flow?

I am simulating Heat Exchanger. I have tried and tested all the methods to resolve this issue from the internet like refining mesh, improving skewness and orthogonal quality ,extending outlet to...

01 March 2021 6,985 3 View

How to calculate the annealing temperature of a primer pair?

I have to amplify a gene and my primers just reached. The Tm for Forward primer is 64.2, and that of reverse primer is 65.5. Can some one suggest how to get the best annealing temperature? Thanks...

01 March 2021 360 7 View

What is recommended for solid domain in ANSYS FLUENT?

Should I mesh the solid domain ? or should I use wall thickness? or Shell conduction? for Heat Transfer between two fluids of a Heat Exchanger. what is recommended?

01 March 2021 9,785 3 View

Can Virtual Servers (remote dekstop manager) run heavy ANSYS Fluent CFD simulation ?

I have a virtual machine. My host Pc specs are not that good thats why i went for virtual servers. so basically my host pc has 8gb of ram with nvidia quadro k2200 4Gb DDR5 GPU ,processor intel...

01 March 2021 8,415 1 View

The reason that the culture of white fungi Contamination with green mold(Trichoderma), the culture autoclave at121 for 15 min. What is it?

Is the period to autoclave not enough? The inoculation in a hood and flame and UV and alcohol.

27 February 2021 9,356 3 View

How to include original NMR data in a manuscript?

hello. i am junior researcher. I received a comment from a reviewer that he could not find NMR data in my submitted paper. I had included the NMR graph with explanation and formula to calculate...

27 February 2021 734 4 View

Does different dilution factors affect negatively on NH3 reading ?

I have a sample of treated water sample & asked to obtain ammonia conc. in sample using a machine with 5-25 ppm detection range. However, upon testing with different dilution factors, all...

27 February 2021 8,483 3 View

Can anyone share his experience regards Smoothing in origin?

I am working on TiO2 composite material and the results of XRD have a lot of small/junk peaks and while I apply a smooth filter in Origin then the other characteristics peaks disappear so anyone...

26 February 2021 8,183 3 View

Would fecal samples stored at -20C for over a year impact metagenomic analysis?

Dear All, I have access to some rodent fecal samples that have been stored at -20C instead of -80C. Anyone have experience with the impact of stowage condition on comparative metagenomic analysis...

01 March 2021 2,512 1 View

How do I check the quality of my viral RNA prior to metagenomic sequencing?

I am doing metagenomic sequencing without enrichment for an RNA virus. After my RNA is extracted from the blood I am doing library prep with the NEBNext Ultra directional RNA library prep kit for...

16 February 2021 5,101 2 View

Does DNA A-tailing survive after agarose gel electrophoresis and purification?

Hi everyone, I need to clone in pGEM-T vector the result of amplifying a metagenomic library by PCR with a high fidelity polymerase but I only want to clone the fragments of an specific size...

04 February 2021 6,051 8 View

How can I solve this problem with agarose gel DNA purification of bigger (1-4kb) fragments ?

Hi everyone, I perform a PCR + Restriction Digestion (single cut, same at both sides) over a metagenomic library. After that, I am trying to purifiy DNA fragments between 1-4kbp long from the...

24 January 2021 2,190 5 View

Could anybody provide insights the best tools to create a custom database for taxonomy assignment of metagenomic data?

I am interested in the different tools that can be used to create custom databases for targeted sequencing and how to trim the databases based on the amplicon size? Also, should custom databases...

02 December 2020 3,105 3 View

Does Shannon index represent largest diversity index when the individual belongs to different species and vice versa?

The shannon wiener index and Simpson indices include the measurement of community heterogeneity. Shannon wiener index bapplied information theory. The main measuring object of information theory...

22 October 2020 1,053 7 View

Is the first clean up necessary in Illumina MiSeq Library Preparation?

I'm trying to streamline my metagenomics protocols for my lab. I have previously followed the 16S protocol...

16 September 2020 5,234 6 View

How to use Vegan::capscale to calculate and plot distance based- redundancy analysis (db-RDA) and add correlation cut-offs in the results?

I have a dataset with relative abundances of Genomes against their COG-ids. It is a large data frame with 4214 rows (COG-ids) and 1313 columns...

13 September 2020 2,334 1 View

Regarding metagenomic contamination?

We have lab established culture setup of marine synechococcus PCC 7002 sp. and heterotrophic bacteria. Recently we did metagenomic analysis of it (sequencing was done by an outside reputed...

12 August 2020 187 11 View

How to find complete protein sequences (not partial) from NCBI database?

I want to generate a custom database of translated proteins involved in a particular process and then blast them against my predicted protein sequences from the metagenome . I have downloaded all...

12 July 2020 2,651 1 View

Abhijeet Singh

There is no single tool for that. And seems like you need some more reading through your reference literature.

Susanta Roy

Use bioinformatics tools like CARD (Comprehensive Antibiotic Resistance Database) [https://card.mcmaster.ca/analyze/rgi] or ResFinder [currently unavailable] to analyze antibiotic resistance for precise gene identification and comparison.

You may also run a local BLAST against a database of interest, such as ResFinder database, if readily available depending on the bioinformatics infrastructure. These tools can assist with identifying and annotating ARGs based on sequence similarity and offer specific details on gene variations, resistance mechanisms, and related metadata for additional investigation and result interpretation.

Sizhong Yang

Prodigal is a frequently used tool to find genes from contigs by a lot of metagenomic pipeline to software. 'Gene comparison', do you mean that you want to know the function of genes? In this step, you need a proper reference database and then annotate your sequences against the database (for example CARD above mentioned), using tools like blastp, diamond, Hmmer, eggNog mapper.