[Genome] EST database

[Kayla Smith]

Hello, Jennifer:

I can't give you a definitive answer, but I can tell you a few things 
about ESTs:

   -the + and - sign in the est tables implicates which strand the EST 

      was mapped to, via sequence identity.

   -transcriptions is always 5' to 3' direction, however ESTs can be
      sequenced from the 5' or the 3' end.

   -the sequence of the ESTs is usually deposited in the read direction,
      that is a 3' EST is reverse-complemented.

   -there is no consistent way in genbank to indicate if a EST is a
     5' or 3' read.

   -for ESTs containing introns, the direction of transcription can
     be determined from the estOrientInfo.intronOrientation column.
     A value < zero, means orientation is reverse of direction of
     transcription, a value > 0 means orientation follows the direction
     of transcription.  A value of 0 means no canonical introns, so we
     can't tell.

   -when rendering the arrows in the browser, if intronOrientation is
     zero, then it checks gbCdnaInfo.direction to see if a read direction
     is recorded.  There is an attempt to parse the direction from
     comments in the genbank entry, so this is very unreliable.

   -finally, only about 1/4 of the single exon ESTs have the direction
     column set in the gbCdnaInfo table, and who know how many of those
     are right.

I hope this information is helpful to you.  Please don't hesitate to 
contact us again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group




Jennifer Chow wrote:
> Hello! 
> 
> I have a question regarding the EST database.  If I am interested in
> determining whether a region is transcribed in both the sense and antisense
> direction, is there a way to determine this by hits to the EST database?
> Does the + and - strand designation give me information about this?
> 
>  
> 
> Thanks!
> 
> Jennifer Chow
> 
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