query regqrding genome feature extraction (gff/gtf) file extraction
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9 weeks ago
abhisek061 ▴ 30

Hi there, Following lines are the portion of a GTF annotation file, can anyone tell me If I want to fetch the promoter/upstream sequences from this file, I am confused a little bit to run a package that asking Enter the length of Upstream Seq. What will be the promoter size/ upstream seq size?

```NZ_CP072122.1 RefSeq gene 21260 22561 . - . ID=gene-J5P21_RS00110;Name=J5P21_RS00110;gbkey=Gene;gene_biotype=protein_coding;locus_tag=J5P21_RS00110;old_locus_tag=J5P21_00110

NZ_CP072122.1 Protein Homology CDS 21260 22561 . - 0 ID=cds-WP_000805827.1;Parent=gene-J5P21_RS00110;Dbxref=Genbank:WP_000805827.1;Name=WP_000805827.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:YP_004997418.1;locus_tag=J5P21_RS00110;product=homoserine dehydrogenase;protein_id=WP_000805827.1;transl_table=11

NZ_CP072122.1 RefSeq gene 22806 23621 . - . ID=gene-J5P21_RS00115;Name=J5P21_RS00115;gbkey=Gene;gene_biotype=protein_coding;locus_tag=J5P21_RS00115;old_locus_tag=J5P21_00115

NZ_CP072122.1 Protein Homology CDS 22806 23621 . - 0 ID=cds-WP_000011164.1;Parent=gene-J5P21_RS00115;Dbxref=Genbank:WP_000011164.1;Name=WP_000011164.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:YP_004997419.1;locus_tag=J5P21_RS00115;product=DsbC family protein;protein_id=WP_000011164.1;transl_table=11 ```

gtf gff • 154 views
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