Direction of assembled genome/output?

[bio_informatics]

Hi All,

Pardon me if this sounds way too dumb query.

Assuming paired end reads are provided, genome is assembled by any tool. Let's say by SPAdes.
What is the direction of assembled contigs and scaffolds?

I found similar question but answer doesn't seem convincing to me.

http://seqanswers.com/forums/showthread.php?t=22956&highlight=strand+assembled

[dpryan]

The answer is correct, it is random. You'd need to use a directional kit, and even then the resulting contigs would still be randomly oriented.

[bio_informatics]

Hi Devon,
Thank you for your reply.

This leads me to another question:
On NCBI, nucleotide database-> search any organism. In fasta file what is the direction of that genome?

[GenoMax]

DNA sequence is conventionally represented in 5' --> 3' direction.

[dpryan]

Assuming you're talking about the "nuccore" database, they're also random. The ratio of + to - orientation will be approximately equivalent to the ratio of orientations of genes in a given organism.

[dpryan]

GenoMax raises a good point and perhaps we're talking past each other. maubp and I are talking about + versus - strand. If you mean, "are the sequences 5'->3' or 3'->5'?", then the answer is always 5'->3'.

[bio_informatics]

Devon
Yes, I was talking about 5'->3' and vice versa. And, yes, I was referring to "nuccore" database.

DNA sequence is conventionally represented in 5' --> 3' direction.

@Genomax - Is that answer applicable to assembled genomes too?
I assume you answered for "nuccore" database query.

[dpryan]

Yes, that applies to assembled sequences as well. DNA should always be presented 5'->3', regardless of application.

[bio_informatics]

Merci beaucoup Monsieurs.
That helps a lot.!

[dpryan]

Happy to help. Should you ever wonder, RNA sequences are also 5'->3' and proteins are N->C (amino to carboxyl terminal). There are a few conventions like this that help prevent migraines

[bio_informatics]

Shall definitely keep in mind, Devon.