How to know CDS and overcome plus/minus stands problems and internal stop codon?

09 November 2017 0 5K Report

I have some gene sequences. I need to get accession number from NCBI but expert advice to provide CDS. And also said those sequences contain mixture of plus/minus stands, and internal stop codon. Sequences, coverage and homology are good enough I supposed.

Need expert suggestions about tools that could be eased my tension!

Badges
Science method

More Javed Foysal's questions See All

Data balancing before test/train split or only training data balancing. which is correct?

While reviewing technical articles, I encounter some papers where authors have used data balancing before splitting test and train (on full data), and some only balanced training data and let the...

04 February 2021 1,446 0 View

DFT Optical calculation and plotting of Real and imaginary Permittivity.??

Dear DFT Community, i have calculated Frequency dependent optical permittivity of Au using (VASP) my INCAR tag includes LOPTICS=.TURE., my OUTCAR has expected frequency dependent IMAGINARY...

30 December 2020 9,543 9 View

Where can I get historic global/national level hydrometeorological data (preferably gridded data)?

Hi, I would like to know where can I get historic global/national (preferably USA) level time-series data for the following (preferably gridded data)? Flood, Drought, Max temperature, Min...

08 November 2020 9,414 6 View

Which Stats to use with categorical IV and DV?

Can you guys tell me which stats should I use when I have both Dependent and Independent variable in categorical form I want to check level of Depression which is categorized as Normal, Mild,...

28 October 2020 3,173 3 View

Effect on MARK4 activity and microtubule of alzheimer mice brain?

I have to determine the effect of some phytoconstituent on MARK4 and microtubule of neuron. How can I do it. I mean do I have to first extract the MARK4 from hippocampus and cortex by RT PCR and...

12 October 2020 653 1 View

Can induce resistance may serve as a source to divert plant photosynthates to defense pathways?

Systemic acquired resistance (SAR) and induced systemic resistance (ISR) are two forms of induced resistance wherein plant defenses are preconditioned by prior infection or treatment that results...

21 September 2020 7,491 3 View

While inserting GOI in pCW57.1 lentiviral plasmid DNA, is it important to delete ccdB gene fragment?

I am facing a problem with the plasmid from addgene (pcW57.1), when transformed into chemically competent DHFa cells, did not give any single colony overnight in ampicilin containing agar...

17 July 2020 8,001 1 View

The reason of incomplete semi-circle?

The Figure in the attachment is taken from the following article: Preparation and characterization of a novel ionic conducting foam-type polymeric gel based on polymer PVdF-HFP and ionic liquid...

09 July 2020 8,409 4 View

Can anyone help to get zeta-potential from my Malvern zetasizer data files? I don't have software anymore?

I have my data files of Malvern zetasizer and I want to get zeta potential from that files anyone who can help me to read original files?

16 February 2020 8,141 5 View

Acceptance possibilities of a Manuscript after initial screening?

How many chances of acceptance of a Manuscript, if editor send it our for peer review after preliminary screening?

12 January 2020 9,834 2 View

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

Is it possible for two human neuronal cell lines to have different gene sequence for the same protein?

I am looking at the ATP1A2 (Sodium/Potassium ATPase alpha subunit 2) in two human neuronal cell lines. Expression levels of this protein seems to be almost equal when detected by one antibody....

01 March 2021 3,607 3 View

Genome-wide gene identification protocol ?

Is there any book chapter/book, webpage or research article available to understand genome-wide gene identification?

28 February 2021 8,095 1 View

Any specific pipeline or parameter to analyse total transcriptomics study of brain tissue samples?

I have two groups of brain samples, control and treated for example. It was total RNA nova seq sequencing. I tried all the available pipeline like: star+rsem+deseq2, Hista+stringtie+cuffdiff,...

27 February 2021 356 6 View

Runs of nucleotides in Sanger sequencing?

I performed site directed mutagenesis, transformation, and then I sent out plasmids for Sanger sequencing and found out that there is extension of DNA just before the stop codon. I am not sure...

27 February 2021 547 3 View

Has anyone used the Illumina ITS1 primer sets?

Hi everyone, Illumina provides a list of primers to amplify with high taxonomic coverage the ITS1 region for further fungal sequencing, but I cannot find the exact amount necessary of each...

25 February 2021 6,969 3 View

Errors in DNA sequences?

I am trying to better understand the scope of DNA replication and sequencing errors, e.g. 1. I have seen similar error rates of 10e4 to 10e5 for cell & instrumental DNA replication,...

24 February 2021 4,397 3 View

RNA-seq DEGs downstream analysis and reporting in literature?

I used EdgeR to get the list of DEGs (differentially expressed genes) from my liver RNA-seq experiment. I have done the gene overrepresentation and GSEA based pathway analysis. I am currently...

23 February 2021 8,969 1 View

Could you please suggests a tutorial or paper or any other materials to learn multiple gene expression in TCGA and GTEx databases?

I would like to analyze multiple gene expressions in normal and cancer tissue by using the data in the TCGA and GTEx databases. Please suggest a tutorial or paper showing step by step analysis of...

23 February 2021 9,007 3 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