Question: Genome DNA sequence pattern matching
0
gravatar for santhoshhegde278
3.0 years ago by
santhoshhegde2780 wrote:

I have a genome sequence in fasta format.As well as I have a DNA pattern.I want to search this patern in the genome.I want just the matching gene header.How to code it in python?can anyone please suggest me?

genome • 1.1k views
ADD COMMENTlink modified 3.0 years ago by Macspider3.3k • written 3.0 years ago by santhoshhegde2780

Blastn, or blastn <options> -outfmt 6

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Buffo1.8k

Thank you very much for your reply

ADD REPLYlink written 3.0 years ago by santhoshhegde2780
1
gravatar for Macspider
3.0 years ago by
Macspider3.3k
Vienna - BOKU
Macspider3.3k wrote:

With literally ANY mapper you will be able to map your pattern sequence against the genome sequence, and it will show in the output the name of the target sequence (i.e. the name of the gene, or scaffold, or transcript depending on what your reference is).

No need to code it yourself!

ADD COMMENTlink written 3.0 years ago by Macspider3.3k

Thank you for your kind reply

ADD REPLYlink written 3.0 years ago by santhoshhegde2780

Is ANY mapper a Application or a online based?

ADD REPLYlink written 3.0 years ago by santhoshhegde2780

I meant that you can use any mapping program you find to do this. It's not the name of a program.

ADD REPLYlink written 2.9 years ago by Macspider3.3k
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