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Ensembl and Gene Prediction Tools output CDS' not divisible by 3

Ensembl and Gene Prediction Tools output CDS' not divisible by 3

I have been looking at a number of different ORF tools such as prodigal and GFF files from databases such as Ensembl and they both report genes/CDS' which are not divisible by 3. Examples below:

Chromosome  Prodigal_v2.6.2 CDS 686 1828    131.5   +   0   ID=1_1;partial=00
Chromosome  ena CDS 686 1828    .   +   0   ID=CDS:AAC71217

Are we supposed to count one end of the CDS differently from another?

1828 - 686 is 1142 1142 modular 3 is 2

Is there something I am not understanding?

Many thanks.

gff cds orf
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updated by ATpoint ATpoint • written by NickJD • NickJD

2 answers

GFF is one-based coordinate. See here Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems. So it is 1828 - 686 +1 = 1143
1143 / 3 = 381

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written by Juke34 Juke34

Many thanks for the answers. While I guessed it was something like this, I could not find any information in the GFF database providers or ORF prediction tools which state what type of system is being use for any particular file/data. I see it is noted in the link that GFF files are 1-based. Is this true for all GFF files and therefore all ORF predictors 'SHOULD' conform to this?

Thanks again.

Note: The website gave an error when I tried to submit a general comment so I responded to the first answer.

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written by NickJD • NickJD

GFF is by definition 1-based, but you have no guarantee that every submitter follows this. If you search long-enough you for sure will find 0-based GFF, bioinformatics is a mess after all :)

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written by ATpoint ATpoint

I agree but I would say this is quite unlikely. As I show here 1-based system is one of the rare thing that was well defined since the beginning of the format in 1997 i.e Integers. <start> must be less than or equal to <end>. Sequence numbering starts at 1, so these numbers should be between 1 and the length of the relevant sequence, inclusive.

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written by Juke34 Juke34

Probably this is a 1-based file so you will need to add +1 to the result which makes it 1143/3=381. GFF files are in fact 1-based.

Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems

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written by ATpoint ATpoint

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