help with Gene Bank annotation and GFF file

Question

[hamaor]

Hi everyone, I downloaded one of E.coli's strains fasta file from here. unfortunately i couldn't find its compatible gff file. in this point if any one can help me find one it could be awsome!

I wrote a script converting fasta to gff3 using gene features fasta file found in the same link. most of gene locations are describes as: [location=376807..377172]

but some of them has this format: [location=join(385707..387164,388426..389874)]

looking further more it seems to belong Pseudogenes. does anyone knows how can i annotate them correctly into my gff file?

thanks a lot

Answer 1

[h.mon]

From the page you viewed, to get the gff3 you have to:

1.) click on the format pop-down menu on the top left and select GenBank (full) 2.) then on the send to pop-down menu on the right select complete record, then on destination select file, finally format select GFF3

Also, from the page you linked, you can select BioProject on the Related information menu on the left (you may have to scroll down a bit), down on the BioProject page there is an Assembly details table, click on the Assembly link on it, then on the Access data menu on the left you will find links to the GenBank and RefSeq ftp sites for this assembly, where you will find the gff (among other files).

[hamaor]

that was extremely helpfull!! i appriciate it!

[h.mon]

If this is the case, please upvote and accept the answer.