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

Once I annotate a genome with PROKKA, where do I uplaod it?

I have annotated a genome successfully with PROKKA. I can upload the genome to NCBI, but I cannot upload the annotation. PROKKA does not produce files in the correct format, and I cannot find any...

29 December 2020 3,976 3 View

How can I design primers of some micro RNAs online ?

How to use NCBI to design primers for specific Micro RNAs for quantitative analysis and how to check the efficacy of the selected primer before working

24 December 2020 180 3 View

How can I know which sequence is the correct one if there are lot of predicted sequence in database for my target gene?

Right now, I want to design qPCR primer for my target gene. But that gene has 21 predicted mRNA sequence in the NCBI database. Most of the sequence names are same but only different location...

23 December 2020 5,531 12 View

Which is the best mitochondrial genome annotation tool? Can anyone provide the list?

I have sequenced the mitochondrial genome of some moths species. I want to annotate and the sequence will submit in the NCBI.

19 November 2020 8,849 1 View

Is it possible to get genomic context data on bulk of accessions?

I'm trying to build local gene synteny to identify homologs between different species. To do that, I've been accessing each individual gene of interest, going into gene view in NCBI and...

04 November 2020 9,038 2 View

Why will only one of three genes amplify CRISPR-Cas9 triple knock out DNA preps?

Working to genotype CRISPR-Cas9 triple mutants. One of the three genes amplifies very well, the other two won't. I have tried three different primer pairs for each of the two genes that won't...

12 October 2020 2,429 3 View

Any suggestions of bioinformatic tools to identify/predict the effect of mutations observed on the function of proteins?

04 October 2020 1,552 4 View

Donwloading from NCBI?

Dear everybody, I'm posting this question because I'm facing a problem with the NCBI database. I should download all the species that belong to a particular phylum (Nematoda) with name and NCBI ID...

30 September 2020 7,808 3 View

How do i determine adjusted p-value for gene expression analysis? and do i use p-value of adjusted p value to choose differentially expressed lncRNA?

how to calculate the value for adjusted p value in gene expression analysis? what is the formula? i'm working on identifiying the level of expression of lncRNA from a datasets deposited in NCBI....

26 September 2020 9,517 4 View