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Question: Genome DNA sequence pattern matching
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gravatar for santhoshhegde278
3.0 years ago by
santhoshhegde278 • 0
santhoshhegde278 • 0 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 COMMENT • link •
modified 3.0 years ago by Macspider • 3.3k • written 3.0 years ago by santhoshhegde278 • 0

Blastn, or blastn <options> -outfmt 6

ADD REPLY • link modified 3.0 years ago • written 3.0 years ago by Buffo • 1.8k

Thank you very much for your reply

ADD REPLY • link written 3.0 years ago by santhoshhegde278 • 0
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gravatar for Macspider
3.0 years ago by
Macspider • 3.3k
Vienna - BOKU
Macspider • 3.3k 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 COMMENT • link written 3.0 years ago by Macspider • 3.3k

Thank you for your kind reply

ADD REPLY • link written 3.0 years ago by santhoshhegde278 • 0

Is ANY mapper a Application or a online based?

ADD REPLY • link written 3.0 years ago by santhoshhegde278 • 0

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

ADD REPLY • link written 2.9 years ago by Macspider • 3.3k
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