[Genome] Yeast splice junctions

[Ann Zweig]

Hello Ilya,

	You can do this using the table browser and custom track tools 
available from the UCSC Genome Browser website.  From the sacCer1 
browser, navigate to the Table Browser tool ("Tables" from the top blue 
navigation bar).

	The table underlying the SGD Gene track, sgdGene, has a column 
containing a comma-separated list of exon starts and exon ends (splice 
sites).  Most of the S. cerevisiae genes in the SGD Gene track consist 
of only one exon.

	Create a list of these exonStarts and exonEnds using the table browser. 
  For help using the Table Browser see: 
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html

The output will look like so:
#name		chrom	strand	exonStarts	exonEnds
YAL068C		chr1	-	1806,		2169,
YAL067W-A	chr1	+	2479,		2707,
YAL067C		chr1	-	7235,		9017,
YAL064W-B	chr1	+	12046,		12427,


	From this file, create a BED file.  Make one BED line for each 
exonStart and one for each exonEnd.  Like so:

chrom chromStart chromEnd name score strand
chr1	1806	1807	YAL068C1	0	-
chr1	2168	2169	YAL068C2	0	-
chr1	2479	2480	YAL067W-A1	0	+
chr1	2706	2707	YAL067W-A2	0	+
chr1	7235	7236	YAL067C1	0	-
chr1	9016	9017	YAL067C2	0	-
chr1	12046	12047	YAL064W-B1	0	+
chr1	12426	12427	YAL064W-B2	0	+


	Now you have a BED file of the single exon at the beginning and end of 
each exon in the SGD Gene track.

	Create a Custom Track from this BED file.  For help creating Custom 
Tracks see: http://genome.ucsc.edu/goldenPath/help/customTrack.html#ADD_CT

	Now go back to the Table Browser, choose your newly-created custom 
track from the list of tables, and choose sequence as the output type. 
On the Sequence Retrieval page, choose:

Add 100 extra bases upstream (5') and 100 extra downstream (3')

	This will give you a file with 200-bp sequence surrounding each exon end.

	Please let us know if you need more detailed instruction.

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu




Ioschikhes, Ilya wrote:
> Hello,
>  
> Please let me know how can I get DNA sequences around S. cerevisiae splice
> junctions (in interval of few hundreds bp).
>  
> Thank you,
>  
> 
> Ilya Ioshikhes, Ph.D.
> Assistant Professor
> Department of Biomedical Informatics,
> Associated Investigator
> 
> Davis Heart and Lung Research Institute,
> Ohio State University
> 3172c Graves Hall
> 333 W. 10th Ave.
> Columbus, OH 43210
> TEL: +1 (614) 292-8929
> Fax: +1 (614) 688-6600
> E-mail: Ilya.Ioschikhes at osumc.edu
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome