84
Body Expression Map of Human Genome
Sese, J.,
Nikaidou, H.,
Kawamoto, S.,
Mine-
saki, Y.,
Morishita, S.,
Okubo, K.
(2001)
BodyMap incorporated PCR-based expression
profling data and a gene ranking system,
Nu-
cleic Acids Res.
29
, 156–158.
Human DNA Sequence Databases
Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J.,
Ostell, J., Wheeler, D.L. (2004) GenBank:
update,
Nucleic Acids Res.
32
, D23–D26.
Birney, E. et al. (2004) Ensembl 2004,
Nucleic
Acids Res.
32
, D468–D470.
Gabriel, S.B.
et al.
(2002)
The
structure
oF
haplotypes blocks in the human genome,
Science
296
, 2225–2229.
Galperin, M.Y. (2004) The molecular biology
database collection: 2004 update,
Nucleic Acids
Res.
32
, D3–D22.
Honkura, T., Ogasawara, J., Yamada, T., Mor-
ishita, S. (2002) The gene resource locator:
gene locus maps For transcriptome analysis,
Nucleic Acids Res.
30
, 221–225.
Jurka, J. (2000) RepBase update: a database and
an electronic journal oF repetitive elements,
Trends Genet.
9
, 418–420.
Karolchik, D. et al. (2004) The UCSC table
browser data retrieval tool,
Nucleic Acids Res.
32
, D497–D501.
Kulikova, T. et al. (2004) The EMBL nucleotide
sequence database,
Nucleic
Acids
Res.
32
,
D27–D30.
Miyazaki, S. et al. (2004) DDBJ in the stream oF
various biological data,
Nucleic Acids Res.
32
,
D31–D34.
Pruitt, K.D., Maglott, D.R. (2001) ReFSeq and
LocusLink: NCBI gene-centered resources,
Nucleic Acids Res.
29
, 137–140.
Sherry, S.T., Ward, M.-H., Kholodov, M., Baker,
J., Phan, L., Smigielski, E.M., Sirotkin, K.
(2001)
dbSNP:
the
NCBI
database
oF
genetic
variation,
Nucleic
Acids
Res.
29
,
308–311.
The International SNP Map Working Group.
(2001) A map oF human genome sequence
variation
containing
1.42 million
single
nucleotide
polymorphisms,
Nature
409
,
928–933.
Thorisson, G.A., Stein, L.D. (2003) The SNP
consortium website: past, present and Future,
Nucleic Acids Res.
31
(1), 124–127.
Wheeler, D.L. et al. (2004) Database resources
oF
the
national
center
For
biotechnology
inFormation: update,
Nucleic Acids Res.
32
,
D35–D40.
Alignment Algorithms
Altschul, S.±.,
Gis, W.,
Myers, E.W.,
Lip-
man, D.J. (1990) Basic local alignment search
tool,
J. Mol. Biol.
215
, 403–410.
Altschul, S.±.,
Madden, T.L.,
SchaFFer, A.A.,
Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.
(1997)
Gapped
BLAST
and
PSI-BLAST:
a
new
generation
oF
protein
database
search programs,
Nucleic Acids Res.
25
(17),
3389–3402.
Needleman, S.B., Wunsch, C.D. (1970) A general
method applicable to the search For similarities
in the amino acid sequence oF two proteins,
J.
Mol. Biol.
48
, 443–453.
Pearson, W.R., Lipman, D.J. (1988) Improved
tools For biological sequence comparison,
Proc.
Natl. Acad. Sci. USA
85
, 2444–2448.
Smith, T.±., Waterman, M.S. (1981) Identifca-
tion oF common molecular subsequences,
J.
Mol. Biol.
147
, 195–197.
Alignment with Large-scale Genomic
Sequences
±lorea, L., Hartzell, G., Zhang, Z., Rubin, G.M.,
Miller, W. (1998) A computer program For
aligning a cDNA sequence with a genomic
sequence,
Genome Res.
8
(9), 967–974.
Kent, W.J.
(2002)
BLAT–the
BLAST-like
alignment tool,
Genome Res.
12
(4), 656–664.
Ma, B., Tromp, J., Li, M. (2002) PatternHunter:
Faster and more sensitive homology search,
Bioinformatics
18
(3), 440–445.
Ogasawara, J., Morishita, S. (2003) ±ast and
sensitive algorithm For aligning ESTs to
human genome,
J. Bioinf. Comp. Biol.
1
(2),
363–386.
Schwartz, S. et al. (2000) PipMaker–a web server
For aligning two genomic DNA sequences,
Genome Res.
10
(4), 577–586.
Schwartz, S.
et al.
(2003)
Human
mouse
alignments with BLASTZ,
Genome Res.
13
(1),
103–107.
Zhang, Z., Schwartz, S., Wagner, L., Miller, W.
(2000)
A
greedy
algorithm
For
aligning
DNA sequences,
J.
Comput.
Biol.
7
(1–2),
203–214.
Oligonucleotide Probe Design
Kaderali, L.,
Schliep, A.
(2002)
Selecting
signature
oligonucleotides
to
identiFy
organisms using DNA arrays,
Bioinformatics
18
(10), 1340–1349.
previous page 758 Encyclopedia of Molecular Cell Biology and Molecular Medicine read online next page 760 Encyclopedia of Molecular Cell Biology and Molecular Medicine read online Home Toggle text on/off