Hello Nandita,
The intronOrientation is a score based on the number of
canonical introns that are observed in the alignment. However,
what is being counted is an indication of the direction of the
mRNA/EST sequence, not which strand it aligns to. Thus a
negative score is an indication that the cDNA sequence is
reverse complemented in Genbank.
The score is roughly a count of the number of apparent canonical
introns. It is incremented by +1 for every gap that appears to be
an intron in the orientation of the sequence and by -1 for every
gap that appears to be an intron that is the reverse-complemented
of the sequence.
While this is computed from the alignment, it doesn't actually
indicate which strand the gene is on. You need both the
alignment strand and the intronOrientation:
pslStrand | intronOrientation | genome strand
+ | > 0 | +
+ | < 0 | -
- | > 0 | -
- | < 0 | +
I hope this information helps make this data sensible for you. Please
don't hesitate to contact us again if you require further assistance,
Kayla Smith
UCSC Genome Bioinformatics Group
On Thu, 15 Jan 2009, Nandita Garud wrote:
> Hello,
>
> I am trying to understand how strand information for mRNAs in the all_mrna
> table is determined. I have followed the FAQ about estOrientInfo, and am I
> correct in understanding that if the intronOrientation field is negative,
> then the strand orientation should actually be opposite of what is listed in
> the all_est table? Is this the same for the mRNAs? How is orientation in the
> all_mrna table determined in the first place? Is it based on the orientation
> suggested by the one who submitted the mRNA to the database, but then
> possibly revised in the mrnaOrientInfo table? If the intronOrientation is 0
> in the mrnaOrientInfo table, how probable would it be that the orientation
> suggested by the all_mrna table is correct?
>
> Thank you,
>
> Nandita
> _______________________________________________
> Genome maillist - [email protected]
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>
_______________________________________________
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http://www.soe.ucsc.edu/mailman/listinfo/genome
