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CILIATEMOLBIO-L  May 2005

CILIATEMOLBIO-L May 2005

Subject:

Gbrowse Sequence Retrieval at TGD

From:

Nick Stover <[log in to unmask]>

Date:

Thu, 26 May 2005 18:55:34 -0700

Content-Type:

text/plain

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Parts/Attachments

text/plain (51 lines)

Dear Ciliate Researchers,

In addition to helping you scan through the annotations of the
Tetrahymena genome, Gbrowse, the genome browser tool supplied by TGD,
provides a handy way to create sequence files.  No more downloading a
500kb scaffold sequence, opening it in Microsoft Word, and ctrl-F
searching for an oligonucleotide sequence at the end of your gene to
get the flanking sequence.  Here’s a quick tutorial to show you how it
works.

 From any gene’s Locus Page, click on the Gbrowse window.  Let’s use
DCR1 (Dicer 1) as an example:
http://db.ciliate.org/cgi-bin/locus.pl?locus=DCR1
After entering Gbrowse, your view will be centered on the TIGR gene
model corresponding to DCR1, in this case PreTt28880.  The DCR1
sequence in GenBank only aligns with half of the PreTt28880 gene model.
  Looks like PreTt28880 probably spans two genes - one of these genes is
obviously DCR1, but what about the other one?

To find out what the gene upstream of DCR1 is, center the Gbrowse view
on the unknown portion of the PreTt28880 gene model.  The easiest way
to do this is to click the “61k” marker on the ruler above the
PreTt28880 graphic.  Zoom in to “Show 5 kb” using the Scroll/Zoom
pull-down menu.  Below the browsing window are options for “Dumps,
Searches and other Operations”.  To retrieve a sequence file of the
genome region depicted in the window (*not the entire scaffold*) select
“Dump Decorated FASTA File” from the first pulldown and click the “Go”
button.  The text shown can be copied and saved into a text editor or
the sequence analysis tool of your choice. The exact coordinates of the
sequence, including the genome scaffold sequence it came from, are also
shown in the FASTA header line.

Unfortunately, it’s hard to tell in this text figure where the
predicted gene regions are.  Back up your browser to adjust some
Gbrowse settings before dumping the Decorated FASTA file again.  Click
the “Configure” button under “Dumps, Searches and other Operations” to
enter this menu.  Set:

‘Output’=html
‘Gene Predictions’=font (red)
‘Tetrahymena GenBank Multiple Hits to Genome (BLAT)’=bkg (yellow)

Click “Go” to paint the sequences matching these tracks with these
different colors.  The sequence comprising PreTt28880, but not part of
the DCR1 cDNA, is now easy to see.  Copy this region into a text editor
or MS Word, chop out the introns, and run a BLASTX with it at NCBI.  (I
got a weak hit to the Plasmodium apicoplast rpoD protein – looks like
it’s probably just a bunch of repetitive, A/T rich DNA).

The Staff at TGD
www.ciliate.org

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