I want to have sequences of a list of genes of several bacterial species. Many of these genes are not available on NCBI and other sources. But the whole genomes of the bacteria are quite a lot there. Anyone knows how
1. I can get sequences of the targeted genes from each whole genome?
2. For the genes available on NCBI, what is the faster way to get sequences of many genes than manually typing name of each genes of each bacterial species on the search tool.
Much appeciated if you can help. Thanks
Dear Prof. Burzynski,
Many thanks for your kindly answer and useful tools for molecular works. Absolutely will learn them soon as I'm new in this field. I'm not really looking for a software tool to get genomic sequences, if there is a simple way to do that.
Could you please tell me which of following ways are correct to obtain sequence of genes that are not available
1. download the whole genome from NCBI, for examples, and then finding the name of those genes on the genome database and collect the sequences from corresponding genes shown there?
2. Align all known sequences of the genes, then blast conserved sequences on the whole genome database to find the location of corresponding genes and get their sequences.
Sincerely thanks!
If you have whole genome in a fasta file, and coordinates for your gene, you can try samtools.
To process multiple genes, you need to wrap it in perl or any such script. Please write back if you need further help.
Vinay
Joy Hinds, I understand your question, and actually I am trying to understand and doing the same. Did you figure it out how to do that?
I am facing the same problem right now. I'm trying to get the sequences of specific genes to run multiple sequence alignment and some of them are available in NCBI as whole genome sequence. If you get the answer for your question please share it with me.
- Badges
- Science method
- Similar topics
- Biological Science
- Genetics
- Genetic Analysis
- genetic techniques
- Sequencing