Bioinformatic Tools in Crop Improvement - Crop Improvement: New Approaches and Modern Techniques - page 54

Table 2.2 Integrative databases for DNA, Gene Sequences and Population Genetics analysis in
plants
Database Name Plant Species/Purpose URL

Home—BioPro-
ject—NCBI

Multi-Purpose site; Over 1000
genomes; plants, animals, bacte-
ria, fungi, virus

http://www.ncbi.nlm.nih.gov/sites/
entrez?db=bioproject

Phytozome v8.0:
Details

Over 31 species of plants; some
software

http://www.phytozome.net/Phyto-
zome_info.php

Gramene Over 29 species of mainly monocots http://www.gramene.org/

BLAST: Basic
Local Align-
ment Search
Tool

Multi-Purpose site for genome com-
parison; plants, animals, bacteria,
fungi, virus

http://blast.ncbi.nlm.nih.gov/Blast.
cgi

GrainGenes Class
Browser:
Marker

Triticeae and Avena site; nearly 200
species

http://wheat.pw.usda.gov/
cgi-bin/graingenes/browse.
cgi?class=marker

PlantGDB—
Resource Plant
Comparative
Genomics

Multi Plant site; 15 dicot, 7 monocot,
3 other plant species

http://www.plantgdb.org/

TreeView Phylogenetic tree software http://taxonomy.zoology.gla.ac.uk/

rod/treeview.html

Rod Page Population genetics, gene diversity

software

http://taxonomy.zoology.gla.ac.uk/
rod/rod.html

Software Softwere site; BLAST, sequence

alignment

http://evolve.zoo.ox.ac.uk/Evolve/
Software.html

LALIGN Server Sequence alignment software http://www.ch.embnet.org/software/

LALIGN_form.html

PopGene Population genetics software http://www2.unil.ch/popgen/soft-

wares/fstat.htm

Arlequin 3.11 Population genetics program http://cmpg.unibe.ch/software/

arlequin3/

ANU Bot Zool Population genetics statistics,

software

http://www.anu.edu.au/BoZo/
GenAlEx/genalex_down-
load_6_1.php

SOPH U AB Population genetics programs http://www.soph.uab.edu/ssg/

linkage/population

Francis Yeh PopGen software http://www.ualberta.ca/~fyeh/

IBD Gene and Distance relations statistics http://www.bio.sdsu.edu/pub/andy/

IBD.html

PRIMER-E Population software and gene diver-

sity statistics and indices

http://www.primer-e.com/

Gramene

An information resource established as a portal for grass species and grass genom-
ics; including genome sequence information. The current version provides data on