Question: Parsing Coding Seq w grep
0
gravatar for maximilian.mayerhofer
2.2 years ago by
maximilian.mayerhofer20 wrote:

Hello,

I have downloaded the E.coli ref strain K-12 MG1655 coding sequence (https://www.ncbi.nlm.nih.gov/nuccore/NC_000913.3). I want to extract certain sequences of genes like gyrA, 23SrRNA,... etc

when using grep like

grep "[gene=gyrA]" EColiK12MG1655_cds.fasta it simply prints everything starting from gyrA (and the letters turn red and White for unknown reasons).

Best regards

gene genome • 453 views
ADD COMMENTlink modified 2.2 years ago by christopher medway440 • written 2.2 years ago by maximilian.mayerhofer20
0
gravatar for christopher medway
2.2 years ago by
Cardiff, UK
christopher medway440 wrote:

I assume you want to extract sequence from the GenBank file. If this is true, there are dedicated libraries that will make this a whole lot easier, See this post

ADD COMMENTlink written 2.2 years ago by christopher medway440
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1182 users visited in the last hour