Get gene sequence for oragnism using python
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9 weeks ago
Ahmed • 0

Hi , If i have the Genus & Species how can i use them in python code to get a gene sequence. For example:

SpecCode: 64588

Genus: Aapticheilichthys

Species: websteri

How can i use these date to get "Cox1" sequence in python ?

Thanks in advance

Bioinformatics python Biopython • 231 views
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You can use this as a base to start!

EFetch: Downloading full records from Entrez

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can you explain more if you can ?

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> >>> from Bio import Entrez
> >>> Entrez.email = "your email here - best guet a account in Entrez/NCBI "  # Always tell NCBI who you are
> >>> handle = Entrez.efetch(db="nucleotide", id="ID for the gene you need", rettype="gb", retmode="text")
> >>> print(handle.read())

EXample of using biopython api to download fasta/genbank files from NCBI You better get one ncbi account and then use the email you login in. Need to choose the database "nucleotides" if you need dna/sequence data. Need a ID for the gene you need data. Need to choose the type of file you need (ig. genbank) etc..

Read the docs here: Entrez biopython

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