3.9.1 Obtain Genomic
Positions of Arabidopsis
Genes from TAIR
Information on genomic positions of all Arabidopsis genes based on
the latest TAIR10 genome build [25] can be found in a general
feature format (gff) file in the TAIR ftp site, ftp://ftp.Arabidopsis.
org/home/tair/Genes/TAIR10_genome_release/TAIR10_gff3.
Download the file TAIR10_GFF3_genes.gff.
3.9.2 Select the Lines
That Have Information on
the Whole Gene Position
$grep ’gene’ TAIR10_GFF3_genes.gff > TAIR10_GFF3_genesonly.gff
3.9.3 Write a Script
Since there is no software for this procedure, we need to write a
script. Here is a sample pseudocode.
#start of the script
snpfile = read in output file from EMMAX filtered by corrected significance
initialize a hash(dictionary)
for snps:
calculate the LD range of overlap by adding (end point) and subtracting (start point)
20kb from the position of the sequence
save the chromosome,LD range of each SNP in the hash
read TAIR10_GFF3_genesonly.gff file
for each snps in hash:
for each gene in gff file:
if same chromosome:
if gene start/end in the LD region:
calculate the shortest distance between gene and the LD region and store
the distance
if the distance is shorter than the distance from the previous gene:
update distance
update mapping of snp to genes
#end of the script
After this step, you will have a list of genes that are associated
with the phenotype.
202
Tak Lee and Insuk Lee