How to retrieve gene sequences from whole genomes
I'm doing MLSA for some bacterial species but I could not get the sequences of many target housekeeping genes of these species on NCBI. The whole genomes of these bacteria are a lot on NCBI. I wonder whether there is any ways to retrieve/extract gene sequences from their whole genome. Anyone knows please help. Many thanks
• 3,426 views
•
link
written
by
nguyen.lamsyd •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How to get the sequence differences between multiple bacterial genomes
written by Rose •
-
How to retrieve/extract specific intergenic regions?
written by geizetomazetto •
-
Download All The Bacterial Genomes (previous versions) From NCBI ftp
written by Ayish •
-
Best way to search for presence of gene in whole genome of related species
written by Mel161803 •
-
Working with PPI using STRING database
written by sharmatina189059 •
-
Get the 16s rRNA gene from NCBI
written by kelvinfrog75 •
-
Identify common genes and their respective DNA sequences
written by sam •
-
SNP calling with fasta files
written by joycewang83 •
-
Whole genome comparison
written by nepgorkhey
-
Downloading All The Incomplete Bacterial Genomes
written by Eric Normandeau
Do you have the chromosomal position of those genes?
Many thanks. sorry I'm new in molecular field, so could you please tell me where I can get the chromosomal position of those genes? and once I got them, what can I do next?
I found that the chromosomal position of the same gene on different species is vastly different and I don't have the position number of each gene on each species chromosome. Much appreciated if you knew any ways to get the genes from the whole genome
Provided the gene names are identical across the bacteria you can find the genomic positions of the genes in the gff files for each genome (NCBI).
You can find the gene sequences for bacterial genomes at Ensembl bacteria. Take a look at the programmatic data access links on that same page.
You can also get similar information from NCBI under this directory hierarchy: https://ftp.ncbi.nih.gov/genomes/genbank/bacteria/