Genome DNA sequence pattern matching

Question

[santhoshhegde278]

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?

[Buffo]

Blastn, or blastn <options> -outfmt 6

[santhoshhegde278]

Thank you very much for your reply

Answer 1

[Matteo Schiavinato]

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!

[santhoshhegde278]

Thank you for your kind reply

[santhoshhegde278]

Is ANY mapper a Application or a online based?

[Matteo Schiavinato]

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