retreive sequence gene

Question

[slimane.khayi]

Hi all, I have a list of genes that I want to retrieve from my genomic sequence in ".gbk" fromat, below example of my list of genes;

length             ID                                 function
1 100    fig|204039.43.peg.1683    FIG00639954: hypothetical protein
1 100    fig|204039.43.peg.3674    hypothetical protein
1 101    fig|204039.43.peg.4227    IncN plasmid KikA protein
2 101    fig|204039.43.peg.968      Antitoxin 1

Thank you for your help

Answer 1

[Manvendra Singh]

convert them into bed format and there is program from bedtools, its fastaFromBed, you can retrieve your sequences.

if they are just four genes then you can also fetch them from UCSC browser.