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CILIATEMOLBIO-L  September 2006

CILIATEMOLBIO-L September 2006

Subject:

Tetrahymena cDNA sequencing update

From:

Ronald Pearlman <[log in to unmask]>

Date:

Fri, 15 Sep 2006 16:41:46 -0400

Content-Type:

TEXT/PLAIN

Parts/Attachments:

Parts/Attachments

TEXT/PLAIN (61 lines)

TIGR has recently completed more EST sequencing and these data have now
been incorporated into the publicly available TBestDB at
http://amoebidia.bcm.umontreal.ca/pepdb/searches/login.php. This is the
same site where EST data have been deposited previously. Click on "Enter
TBestDB" (all Tetrahymena data are public so there is no need for a
password) and then scroll down to Tetrahymena thermophila, click there,
and you will have access to the data and statistical analysis of the data.
To BLAST the EST data, you will need to use ANABENCH BLAST server at
http://anabench.bcm.umontreal.ca/anabench/.

Some resequencing has been done, some of this from both directions
(initial sequencing was single pass from one direction), of "old"
libraries and some data are from the sequencing of a new starved cell
library. An overview of new data on the site are as follows:

We previously had 33,304 sequences providing 9,062 clusters. With the new
data, we now have an additional 19,741 sequences (52,745 total) and 2,872
additional clusters (11,934 total).

We have 14,235 additional sequences from the conjugative library, 7,618
sequenced with the forward primer and 6,617 with the reverse primer. There
are 1,025 new sequences from the normalized vegetative large fraction
library, 761 sequenced with the forward primer and 264 sequenced with an
Oligo dT reverse primer.

A new starved cell library was prepared (TIGR) and we have 4,234 sequences
from that. 3600 are sequenced with a forward primer and 634 with two
different reverse primers. As yet, we have not analyzed how many new
clusters come from the starved cell library. The expectation is that most
of the new clusters should be from this library.

Data can be analyzed as in the past. Please access archived messages
on this listserve for more detail or contact myself or Jyoti Garg
([log in to unmask]) in my lab for additional detail or with any
questions. Each EST can be traced to a specific library.

I trust this information will be useful to the community. Good luck, happy
hunting, and let myself or Jyoti know if you have any questions.

We are very pleased that the TIGR group and those involved with the
TBestDB continue to work together to make these important resources
available to the community. The TBestDB is a continuation of the initially
Genome Canada funded Protist EST Project (PEP) that initiated the major
Tetrahymena EST sequencing effort. It is important that new data be added
to existing data and remain transparently available to the community. We
acknowledge and thank all involved in making this possible and look
forward to providing new updates to the community as additional EST
sequencing is done at TIGR.

       Ron


Dr. Ronald E. Pearlman           [log in to unmask]
University Professor
Dept. of Biology
Dean
Faculty of Graduate Studies
Director, Core Molecular Biology Facility
York University
4700 Keele St., Toronto, Ontario, Canada M3J 1P3
Phone:416-736-5241; FAX:416-736-5698

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