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Chromosome Reports Description
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| In effort to allow the users of the
draft assembly
sequence produced by NCBI and the
UCSC Human
Genome Browser to evaluate the quality of the assembled human
genome, we have created a series of web pages that show comparisons
with existing genome-wide sequence tagged sites (STS) maps, BAC end
sequence pair information, and calculated clone sequence
overlaps. Using this resource, areas in the genome of special research
interest can be examined to determine whether the sequence information
is accurate and reliable before expensive and time-consuming
experiments are undertaken. Below is first a bit of background on the
current process for creating the assembled sequence followed by a
description of what is contained within these web pages
As sequencing efforts are being concentrated on producing finished
sequence and identifying clones to fill in current gaps, the
responsibility for each chromosome has been assigned to a particular
sequencing center and are as follows:
| Sequencing Center | Contact | Chromosomes |
|---|
| Baylor College of Medicine | Steve Scherrer | 3, 12 |
| Genoscope National Sequencing Centre | Jean Weissenbach | 14 |
| Dept. of Energy Joint Genome Institute | Joe Monforte | 5 |
| Los Alamos National Laboratory | Norman Doggett | 16 |
| RIKEN Human Genome Research Group | Todd Taylor | 11, 21 (21 consortium) |
| Sanger Centre | Jane Rogers | 1, 6, 9, 10, 13, 20, 22, X |
| Stanford Human Genome Center | Jane Grimwood | 19 |
| Washington University Genome Sequencing Center | Rick Wilson | 2, 4, 7, Y |
| Whitehead Institute | Chad Nausbaum | 8, 15, 17, 18 |
More information about the sequencing effort can be found at Ensembl's
Human Assemblies Genome
Server and NCBI's Human Genome
Sequencing web sites.
Each center is responsible for producing a minimal tiling path
(TPF) map representing their current ordering of clones across
the chromosomes for which they are responsible. These clones need not
be sequenced, yet, and thus sequence for them may not be deposited
into GenBank.
Beginning with the December 22nd freeze, UCSC has switched to
using the NCBI assembly. The reports generated here, then, are based
on NCBI's build30 assembly. This is built using the TPF clone maps as
the main input source. UCSC will no longer produce an assembled sequence
of their own.
For the draft assembly sequence, web pages have been created
showing how each of these compare with other sources of information.
Currently, the user can view the correspondence between these clones
maps and sequence-tagged site STS maps in both a
scatter plot and in a tabular format. The STS maps
employed in this analysis include the
Genethon and
Marshfield
genetic maps, the
Whitehead
Institute YAC map, and the NCBI GeneMap99 GB4 and
G3,
Whitehead
Institute, and
Stanford
TNG radiation hybridization (RH) maps. In addition, there is BAC End Pairs and
Clone Overlap information. A
Summary Page is provided that
shows a high-level view of all of this information for each
chromosome. Multiple sources of information are used because each has
errors. With this combination, it can be determined often whether
there is an error in one of the clone maps, or it is a mistake in the
conflicting information.
Feedback concerning both these webs pages and the underlying
clone maps on which they are based is encouraged. If there appears to
be an error in a TPF clone map, please alert the chromosome
coordinator for the corresponding chromosome as listed in the table
above. Please include supporting evidence showing why the current map
is not accurate.
NOTE: The TPF maps displayed here represent the version used
for a particular assembly. These maps are constantly being updated by
each of the sequencing centers as new information becomes available.
For general comments regarding these web pages, please contact
Terry Furey at UC Santa Cruz.
Terry Furey
Last modified: Fri Jul 12 11:29:06 PDT 2002
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