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Chromosome Reports Description
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In effort to allow the users of the human genome sequence
and the
UCSC Human
Genome Browser to evaluate the quality of the human
genome sequence, 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.
Prior to the April 10, 2003 sequence (build33), the
sequence was assembled computationally based on clone maps created by
sequencing centers. Now that the genome is essentially finished, sequencing
centers provide the complete final sequence - no assembly is performed.
Below is first a bit of background on the
previous process for creating the assembled sequence followed by a
description of what is contained within these web pages
As sequencing efforts became focused on producing finished sequence
and identifying clones to fill in remaining gaps, the responsibility for each chromosome
was assigned to a particular sequencing center, 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 | Eddy Rubin | 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
NCBI's Human Genome Sequencing web site.
Each center has been 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.
For the August 2001 assembly, the framework map on which the UCSC assembly is based shifted
from solely the Washington University
accession map to a combination of the TPF maps and the WashU accession map.
Just like how a snapshot of sequences currently deposited in GenBank ("a freeze") is taken when
creating an assembly, a snapshot of the TPF maps for each chromosome is taken.
Since the TPF maps are a minimal tiling
path possibly containing unsequenced clones not in the GenBank freeze,
they are combined with the the WashU
accession map using a dynamic programming algorithm developed at Ensembl to produce the final framework
clone map on which the assembly is based.
The December 2001 and April 2002 assemblies were created by NCBI using no clone maps. Starting with the December 2001,
UCSC no longer created a separate assembly of the genome.
The June 2002 and November 2002 assemblies were created by NCBI using TPF clones maps provided
by the sequencing centers.
For each of 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 often be determined whether there is
an error in one of the clone maps or a mistake in the conflicting information.
Feedback concerning both these webs pages and the underlying chromosome sequence on which they are based
is encouraged. If there appears to be an error in a particular chromosome, 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.
For general comments regarding these web pages, please contact
Terry Furey at UC Santa Cruz.
Terry Furey
Last modified: Tue Feb 26 14:01:09 PST 2002
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