2. Type “ABI3” into the box and click on the magnifying glass.
3. On the resulting page, click on the first result, which should be
labeled AT3G24650, of type “Gene.”
4. The link takes us to ThaleMine, which is a module of Araport.
5. A summary of the information about the ABI3 gene product is
presented at the top of the page.
6. Click on “Genomics” on the “Quick Links” bar. You can
obtain the DNA sequence of ABI3 by clicking on the
“FASTA” button here.
7. If you click on “Proteins” and click on the first label
(ABI3_ARATH) under “DB Identifier” you will get more
information about the protein. A similar “FASTA” button
exists to download the ABI protein’s amino acid sequence.
3.1.2 1001 Genomes
The 1001 Genomes project provides data on more than 1001
strains (accessions or genotypes) of Arabidopsis thaliana collected
from around the world [11]. A single reference genome is now
thought to not be sufficient to represent the genes of an entire
species, considering how many polymorphisms have been found to
occur across the vast number of sequenced accessions. With the
PolyMorph tool we can examine if there are any synonymous or
non-synonymous variants, or small insertions or deletions in naturally occurring alleles of a gene of interest based on the sequence
data that have been generated by the 1001 Genomes project.
1. Go to http://tools.1001genomes.org/polymorph/. Under
the “Locus” parameter, input “AT3G24650” as the “Gene
Identifier.” Select “AT3G24650.1.”
2. Under “Filter,” set the “Variant Type” to “SNPs,” “Impact” to
“All,” and “Effect Type” to “All.” Click on the “Accessions”
parameter to see some of the accessions, but do not deselect
any accessions. You can go to http://1001genomes.org/acces
sions.html to learn more about them. Click Search.
3. You will see a table of results, sorted by position, although you
can change this by clicking on the table headers (this will take a
moment). Click on Strain to sort by strain number. The first
sequenced Arabidopsis strain was Col-0. In 1001 Genomes its
strain number is 6909. Note that polymorphisms for Col-0 will
not be present in the table as the polymorphisms are presented
relative to this strain!
4. Look at the “Effect Type” column and click on the table rows
to see details. In particular, look for an effect where the impact
is “MODERATE.” These kinds of mutations are typically
non-synonymous nucleotide changes that result in a changed
amino acid in one or more strains of Arabidopsis thaliana.
These may subtly change the properties of the protein. For
Arabidopsis Bioinformatics
29
3. On the resulting page, click on the first result, which should be
labeled AT3G24650, of type “Gene.”
4. The link takes us to ThaleMine, which is a module of Araport.
5. A summary of the information about the ABI3 gene product is
presented at the top of the page.
6. Click on “Genomics” on the “Quick Links” bar. You can
obtain the DNA sequence of ABI3 by clicking on the
“FASTA” button here.
7. If you click on “Proteins” and click on the first label
(ABI3_ARATH) under “DB Identifier” you will get more
information about the protein. A similar “FASTA” button
exists to download the ABI protein’s amino acid sequence.
3.1.2 1001 Genomes
The 1001 Genomes project provides data on more than 1001
strains (accessions or genotypes) of Arabidopsis thaliana collected
from around the world [11]. A single reference genome is now
thought to not be sufficient to represent the genes of an entire
species, considering how many polymorphisms have been found to
occur across the vast number of sequenced accessions. With the
PolyMorph tool we can examine if there are any synonymous or
non-synonymous variants, or small insertions or deletions in naturally occurring alleles of a gene of interest based on the sequence
data that have been generated by the 1001 Genomes project.
1. Go to http://tools.1001genomes.org/polymorph/. Under
the “Locus” parameter, input “AT3G24650” as the “Gene
Identifier.” Select “AT3G24650.1.”
2. Under “Filter,” set the “Variant Type” to “SNPs,” “Impact” to
“All,” and “Effect Type” to “All.” Click on the “Accessions”
parameter to see some of the accessions, but do not deselect
any accessions. You can go to http://1001genomes.org/acces
sions.html to learn more about them. Click Search.
3. You will see a table of results, sorted by position, although you
can change this by clicking on the table headers (this will take a
moment). Click on Strain to sort by strain number. The first
sequenced Arabidopsis strain was Col-0. In 1001 Genomes its
strain number is 6909. Note that polymorphisms for Col-0 will
not be present in the table as the polymorphisms are presented
relative to this strain!
4. Look at the “Effect Type” column and click on the table rows
to see details. In particular, look for an effect where the impact
is “MODERATE.” These kinds of mutations are typically
non-synonymous nucleotide changes that result in a changed
amino acid in one or more strains of Arabidopsis thaliana.
These may subtly change the properties of the protein. For
Arabidopsis Bioinformatics
29