Number of required occurences | Description | |||||||||

mipe | exactly one | |||||||||

version | exactly one | version number of the MIPE format | ||||||||

pcr | one or more | one for each PCR product | ||||||||

id | exactly one | ID of the PCR product | ||||||||

modified | one or more | dates that this record has been modified | ||||||||

project | zero or more | project(s) that this record belongs to | ||||||||

researcher | one or more | researcher(s) involved in designing/running the PCR | ||||||||

species | one or more | species on which the PCR experiment is performed | ||||||||

design | exactly one | data pertaining to the design of the PCR | ||||||||

source | exactly one | initial sequence on which the PCR primers were designed | ||||||||

accession/file/seq | exactly one | reference to the source DNA sequence | ||||||||

name | zero or one | e.g. gene-name | ||||||||

species | zero or one | species on which the PCR experiment is performed | ||||||||

type | zero or one | genomic or cDNA | ||||||||

remark | zero or more | |||||||||

range | zero or one | part of the source sequence that will be amplified by the PCR product (in nucleotide positions) | ||||||||

seq | zero or one | sequence expected to be replicated (= part of the source sequence) | ||||||||

primer1 | zero or one | forward primer | ||||||||

oligo | zero or one | internal ID of oligo | ||||||||

seq | zero or one | sequence of primer | ||||||||

tm | zero or one | melting temperature of primer | ||||||||

primer2 | zero or one | reverse primer | ||||||||

oligo | zero or one | internal ID of oligo | ||||||||

seq | zero or one | sequence of primer | ||||||||

tm | zero or one | melting temperature of primer | ||||||||

profile | zero or one | PCR profile | ||||||||

name | zero or one | name of PCR profile | ||||||||

predenaturation | zero or one | predenaturation step | ||||||||

temp | exactly one | |||||||||

time | exactly one | |||||||||

cycle | zero or more | data for each cycle | ||||||||

number | exactly one | number of cycles | ||||||||

denaturation | exactly one | denaturation step | ||||||||

temp | exactly one | |||||||||

time | exactly one | |||||||||

annealing | exactly one | annealing step | ||||||||

temp | exactly one | |||||||||

time | exactly one | |||||||||

elongation | exactly one | elongation step | ||||||||

temp | exactly one | |||||||||

time | exactly one | |||||||||

postelongation | zero or one | postelongation step | ||||||||

temp | exactly one | |||||||||

time | exactly one | |||||||||

remark | zero or more | |||||||||

use | zero or one | contains information on the results of a PCR resequencing experiment | ||||||||

seq | exactly one | sequence | ||||||||

revcomp | exactly one | whether or not this sequence is the reverse complementary of the sequence in the design part | ||||||||

snp | zero or more | single-nucleotide polymorphisms | ||||||||

id | exactly one | |||||||||

pos | exactly one | position of the SNP on the use sequence | ||||||||

pos_design | zero or one | position of the SNP on the design sequence | ||||||||

pos_source | zero or one | position of the SNP on the sourcesequence | ||||||||

amb | zero or one | ambiguity code of the SNP | ||||||||

rank | zero or one | if found by polyphred: rank of the SNP (ranges from 1 to 6) | ||||||||

assay | zero or more | SNP genotyping assay | ||||||||

type | exactly one | either RFLP or SBE (single-base extension) | ||||||||

id | exactly one | |||||||||

enzyme | zero or one | if type was RFLP: restriction enzyme | ||||||||

oligo | zero or one | internal ID of oligo | ||||||||

specific | zero or one | if type was SBE: sequence of the SBE primer that is specific | ||||||||

tail | zero or one | if type was SBE: sequence of optional tail that is non-specific | ||||||||

strand | zero or one | if type was SBE: strand that the SBE primer will attach to (relative to the sequence in the use part) | ||||||||

remark | zero or more | |||||||||

remark | zero or more | |||||||||

sample | zero or more | if resequenced on different individuals | ||||||||

id | zero or one | |||||||||

file | zero or one | ab1-file containing the sequence for this particular individual | ||||||||

genotype | zero or more | genotypes for this individual | ||||||||

snp_id | exactly one | ID of a SNP as mentioned above | ||||||||

amb | exactly one | ambiguity code for that SNP in this individual | ||||||||

remark | zero or more | |||||||||

remark | zero or more | |||||||||

remark | zero or more | |||||||||

remark | zero or more | |||||||||

remark | zero or more | |||||||||

remark | zero or more |