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7.3 years ago
nguyen.lamsyd
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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
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/
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).