query regqrding genome feature extraction (gff/gtf) file extraction
0
0
Entering edit mode
2.0 years ago

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 • 395 views
ADD COMMENT

Login before adding your answer.

Traffic: 1192 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6