Introduction of genome database in application, Lecture notes of Genomics

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GENOME DATABASES

GENOME DATABASES

WHAT IS A GENOME?

WHAT IS A GENOME?

Organism’s whole hereditary

Organism’s whole hereditary

information

information

includes both the

includes both the genes

genes and the

and the

non-coding sequences

non-coding sequences of the DNA

of the DNA

complete

complete

DNA sequence

DNA sequence

of one set of

of one set of

chromosomes

chromosomes .

.

term was coined in 1920 by

term was coined in 1920 by

Hans Winkler

Hans Winkler

Cont,

Cont,



Plant

Plant



USDA/ARS/National Agricultural Library Plant Genome Data

USDA/ARS/National Agricultural Library Plant Genome Data



(NAL) National Agricultural Library; Plant Genomes(NAL) National Agricultural Library; Plant Genomes



AAtDB browse An Arabidopsis thaliana genome database at NAL -

AAtDB browse An Arabidopsis thaliana genome database at NAL -

query query



AAtDB at Harvard U. -

AAtDB at Harvard U. - Search

Search



Arabidopsis Expressed Sequence Tags (EST's)

Arabidopsis Expressed Sequence Tags (EST's)



Arabidopsis Information Management System (AIMS)

Arabidopsis Information Management System (AIMS)



U. Minnesota Arabidopsis cDNA sequencing ProjectU. Minnesota Arabidopsis cDNA sequencing Project



Alfagenes browse Alfalfa genome database at NAL

Alfagenes browse Alfalfa genome database at NAL query

query



BeanRef

BeanRef



BeanGenes browse Bean genome database at NAL

BeanGenes browse Bean genome database at NAL query

query



ChlamyDB browse

ChlamyDB browse Chlamydomonas database at NAL

Chlamydomonas database at NAL query

query



CottonDB browse Gossypium sp. database at NAL

CottonDB browse Gossypium sp. database at NAL query

query



GrainGenes browse

GrainGenes browse query

query



MaizeDB browse Maize genome database at NAL

MaizeDB browse Maize genome database at NAL query

query



MaizeDB Maize Genome Database

MaizeDB Maize Genome Database



RiceGenes browse Rice genome database at NAL

RiceGenes browse Rice genome database at NAL query

query



Japan Rice Genome Research Program (RGP)

Japan Rice Genome Research Program (RGP)



SorghumDB browse Sorghum bicolor database at NAL

SorghumDB browse Sorghum bicolor database at NAL query

query



SoyBase browse Soybean genome database at NAL

SoyBase browse Soybean genome database at NAL query

query



TreeGenes browse Forest trees database at NAL

TreeGenes browse Forest trees database at NAL query

query



Mendel browse Plant-wide gene names database at NAL

Mendel browse Plant-wide gene names database at NAL

query

query



Fungal

Fungal



Mycology at Cornell

Mycology at Cornell



Saccharomyces genomic database

Saccharomyces genomic database



LISTA A Compilation of Sequences from Saccharomyces

LISTA A Compilation of Sequences from Saccharomyces



Yeast Protein Database (YPD)

Yeast Protein Database (YPD)



MycDB Mycobacterium Database

MycDB Mycobacterium Database



MycDB browse at NAL

MycDB browse at NAL query

query



Candida albicans

Candida albicans



FGSC Fungal Genetics Stock Center

FGSC Fungal Genetics Stock Center



Eschericia coli

Eschericia coli



EcoCyc: Encyclopedia of E. coli Genes and Metabolism

EcoCyc: Encyclopedia of E. coli Genes and Metabolism



ECDC (

ECDC (

E. coli

E. coli Database Collection)

Database Collection)



Other Prokaryotes

Other Prokaryotes



Normalized Gene Designation Database (NGDD)

Normalized Gene Designation Database (NGDD)

http://www.bioscience.org/

http://www.bioscience.org/

http://genome.ucsc.edu/

http://genome.ucsc.edu/

www.

www. genomes

genomes online.org/

online.org/

http://www.ebi.ac.uk/ensembl/

http://www.ebi.ac.uk/ensembl/

www.genomenewsnetwork.com

www.genomenewsnetwork.com