Body Expression Map of Human Genome
77
is qualitative. In contrast, body-mapping projects are designed to clarify the
differences of cells or tissues in terms of gene expression proFles; thus, they
have to be quantitative at every step during the experiment. Integration of millions
of EST alignments on the human genome needs browsers that facilitate efFcient
searching and browsing of an enormous quantity of EST alignments. To achieve
this goal, it is essential to meet speciFc computational requirements, such as the
acceleration of sensitive-but-slow (dynamic programming) alignment algorithms,
and the resolution of EST orientations. Genome browsers such as Ensembl, UCSC,
NCBI, and GRL support these functions.
1
Overview
Nearly two years after the publication of the
historic paper on the human draft genome
sequence and initial analyses, sequenc-
in
go
fm
o
s
to
fth
eeu
ch
r
om
a
t
inr
eg
i
on
of the human genome is near completion,
ushering in the age of genome science (an-
nouncement of the completion of human
genome was made in April 2003). The com-
plete sequence of the human genome or
any genome will provide researchers and
the society with valuable information con-
cerning the positions and primary struc-
tures of genes, genetic markers, repetitive
sequences, functional elements, and lines
of evidence of chromosomal rearrange-
ment during human evolution. Many of
these aspects are, at present, incompletely
understood, and await intensive studies
in the future by scientists from various
disciplines. Structural analyses of other
functionally important elements, such as
centromeric and telomeric regions that
are buried in heterochromatin must wait
for a longer period. In addition, the se-
quences and position data will be updated
for many years.
Howeve
r
,thesequen
cewew
i
l
lseein
a database of a human genome is a sort
of patchwork of several genomes because
of the technical considerations relating to
the sequencing and preparation of DNA
materials. Thus, the sequence in the public
databases (GenBank, DDBJ, and EMBL)
should be regarded as a reference set for
our genome. It is very important, when
we look at the sequence data, that we keep
in mind that the human genome does
not reflect the heterogeneity of human
population. Because of this, variation
studies, such as identiFcation of Single
nucleotide polymorphisms (SNPs) and
typing of haplotype patterns using various
human subpopulations will be important
to identify the functional differences linked
with speciFc genomic variation. In other
words,
functional
studies
of personal
differences will be the basis of the medical
and pharmaceutical studies in the future.
In this chapter, a set of databases and
tools that we believe will be useful to
such studies will be presented. Statistical
and mapping data presented in the later
section of this chapter are calculated using
human genome assembly data available in
January 2003.
1.1
Genes and Genome
One of the major objectives of the Hu-
man Genome Project (HGP) was to list
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