Best way to download a subsection of a genome that matches a search query on NCBI's Blast?
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3.1 years ago
Tom ▴ 20

I have a gene section of a cow genomic sequence (X59856) coding for a milk protein and I want to find the corresponding gene clusters in mouse, and human. What's the best way to slice out and download just the subsection of the aligned portion that matched? I would also want about 10,000 nucleotides up/downstream to get the flanking regions?

blast ncbi alignment • 605 views
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One option is to see if the protein is present in pre-computed alignments in NCBI Homologene (e.g. this is for milk protein of some kind https://www.ncbi.nlm.nih.gov/homologene/4334 ). You can then take the proteins and map then back on the genome sequence. Both Ensembl (Compara) and UCSC also have precomputed sections like this.

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Can you be a lot more specific?

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NCBI's datasets tool can retrieve ortholog data: https://ncbiinsights.ncbi.nlm.nih.gov/2021/02/23/datasets-orthologs

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