GFF3 Not Unique ID

Question

[navillusol858]

Hello, I created a GFF3 file using the bp_search2gff.pl, I had Blastx tab format and used this to create a GFF3 file. I ran my GFF3 file through http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online to check if it is valid.

I wish to add this GFF3 file to gbrowse later.

I get an error non unique ID, I am wondering if there is any easy way to overcome this issue? Google searches have proved fruitless.

Thanks for the help

[Juke34]

Could you add some lines of your gff file to see how it looks ?

Theoretically this problem comes from the ID feature present in the 9th column of your file...

[navillusol858]

Sure, this is the first couple of lines. When I run my GFF3 file through the validator I get this error,

Line Number  Error/Warning
-----------  -------------
3            [ERROR]   non-unique id (id: Contig1)
5            [ERROR]   non-unique id (id: Contig1)
7            [ERROR]   non-unique id (id: Contig1)
9            [ERROR]   non-unique id (id: Contig1)

The file itself looks like:

##gff-version 3
gi|47221249|emb|CAG13185.1|    BLASTX    similarity    5151    5409    228    .    0    Parent=Contig1;Target=Sequence:Contig1 160 933
gi|47221249|emb|CAG13185.1|    BLASTX    match    5151    5409    228    .    1    ID=Contig1
gi|498932434|ref|XP_004540187.1|    BLASTX    similarity    7891    8149    226    .    0    Parent=Contig1;Target=Sequence:Contig1 160 933
gi|498932434|ref|XP_004540187.1|    BLASTX    match    7891    8149    226    .    1    ID=Contig1
gi|498932432|ref|XP_004540186.1|    BLASTX    similarity    7943    8201    226    .    0    Parent=Contig1;Target=Sequence:Contig1 160 933
gi|498932432|ref|XP_004540186.1|    BLASTX    match    7943    8201    226    .    1    ID=Contig1
gi|348511029|ref|XP_003443047.1|    BLASTX    similarity    7905    8163    226    .    0    Parent=Contig1;Target=Sequence:Contig1 160 933
gi|348511029|ref|XP_003443047.1|    BLASTX    match    7905    8163    226    .    1    ID=Contig1
gi|443699164|gb|ELT98774.1|    BLASTX    similarity    1    105    57.8    +    0    Parent=Contig2;Target=Sequence:Contig2 105 419
gi|443699164|gb|ELT98774.1|    BLASTX    match    1    105    57.8    +    1    ID=Contig2

Thank you for your help.

[Juke34]

Your gff file is not correct ... there is a problem in the script "bp_search2gff.pl" that you used or with the data that you gave as input. The Id in the 9th column should be Uniq. Try an other script, there is many scripts to do this kind of work...

http://www.sequenceontology.org/resources/gff3.html