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Genome DNA sequence pattern matching

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
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updated by Matteo Schiavinato Matteo Schiavinato • written by santhoshhegde278 • santhoshhegde278

Blastn, or blastn <options> -outfmt 6

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written by Buffo Buffo

1 answer

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!

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written by Matteo Schiavinato Matteo Schiavinato

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

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written by Matteo Schiavinato Matteo Schiavinato

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