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Arabidopsis Genetic Markers - Raw Data and Physical Positions on Genome


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original data source: 

www.arabidopsis.info

ftp.arabidopsis.org

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original data files (DNA sequences):

DL_Raw_Data_RI_markers.tfa

DL_Raw_Data_chrom2_markers.tfa

DL_Raw_Data_chrom4_markers.tfa

DL_Raw_Data_markers_with_flanking_seqs.tab

DL_Raw_Data_primers.tfa


original locus file (raw marker scores):

DL_RIL_Data.may2001.loc [ 1357 markers total ]

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original data files (DNA sequences) were modified into files in FASTA format:

DL_Raw_Data_RI_markers.tfa.UPPER.fasta

DL_Raw_Data_chrom2_markers.tfa.UPPER.fasta

DL_Raw_Data_chrom4_markers.tfa.UPPER.fasta

DL_Raw_Data_markers_with_flanking_seqs.tab.UPPER.fasta

DL_Raw_Data_primers.tfa.UPPER._A.fasta

DL_Raw_Data_primers.tfa.UPPER._B.fasta

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original locus file was modified; it contains markers only if DNA sequence is available:

DL_RIL_Data.may2001.MM.loc [ 563 markers total ]

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FASTA files were combined into three sets and BLAST-ed against Arabidopsis assembly;
BLAST output was parsed using tcl_blast_parser:

ath_NCBI_genome.fasta

[ set #2 ]
DL_Raw_Data_xset_N3.seqs.mod
DL_Raw_Data_xset_N3.seqs.mod.xproc.vs.ath_NCBI_genome.BlastN
DL_Raw_Data_xset_N3.seqs.mod.xproc.vs.ath_NCBI_genome.BlastN.info2

[ set #3 ]
DL_Raw_Data_markers_with_flanking_seqs.tab.UPPER.fasta
DL_Raw_Data_markers_with_flanking_seqs.tab.UPPER.vs.ath_NCBI_genome.BlastN
DL_Raw_Data_markers_with_flanking_seqs.tab.UPPER.vs.ath_NCBI_genome.BlastN.info2

[ set #1 ]
DL_Raw_Data_primers.tfa.UPPER._A.fasta
DL_Raw_Data_primers.tfa.UPPER._A.vs.ath_NCBI_genome.BlastN
DL_Raw_Data_primers.tfa.UPPER._A.vs.ath_NCBI_genome.BlastN.info2
DL_Raw_Data_primers.tfa.UPPER._B.fasta
DL_Raw_Data_primers.tfa.UPPER._B.vs.ath_NCBI_genome.BlastN
DL_Raw_Data_primers.tfa.UPPER._B.vs.ath_NCBI_genome.BlastN.info2

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*.info2 files were analysed and modified using MS excel spreadsheets:

x-phys-coords-set-1.txt
x-phys-coords-set-2.txt
x-phys-coords-set-3.txt

x-phys-coords-all-sets-mod-uniq.txt file is a final result of analysis

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physical coordinates of markers per linkage group:
[ 1-st column: linkage group | 2-nd: marker id | 3-d: position in Mb | 4-th: nt position ]

x-phys-coords-ath-lg1.map
x-phys-coords-ath-lg2.map
x-phys-coords-ath-lg3.map
x-phys-coords-ath-lg4.map
x-phys-coords-ath-lg5.map

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