PMSeeker

Overview

PMSeeker provides a scheme based on the greedy algorithm and the exhaustive algorithm to screen low-redundancy marker set for parentage assignment (PMS) of diploid species. The scheme can effectively reduce the number of markers needed in a parentage assignment. The exhaustive algorithm can find out the optimal PMS by traversing all marker combinations, and cannot handle more than 20 markers due to the huge number of combinations. Therefore, the greedy algorithm has to be adopted, though it is only capable of obtaining the local-optimal PMS. Detailed information about the two algorithms is available in introduction.pdf.

Data for peer review: article_data.zip

Citation: Xia L, Shi M, Li H, Zhang W, Cheng Y, Xia X-Q. PMSeeker: a scheme based on the greedy algorithm and the exhaustive algorithm to screen low-redundancy marker sets for large-scale parentage assignment with full parental genotyping. Biology, 2024, 13(2): 100. doi.org/10.3390/biology13020100

Run

1. [Required] Upload the file for parent genotype information: Note: This is a comma-delimited file, in which the genotypes of diploid markers are represented by '.A' and '.B' as in the example file.
2. [Optional] Upload the file specifying parent genders or families ( Gender Family ): Note: The "Gender file" (example) is a TAB-delimited file with one column specifying the gender ("female" or "male") of parents in a random mating population; and the "Family file" (example) is TAB-delimited file where each row stands for one family. Note: The "Gender file" (example) is a TAB-delimited file with one column specifying the gender ("female" or "male") of parents in a random mating population; and the "Family file" (example) is TAB-delimited file where each row stands for one family.

1. [Required] Upload the file for parent genotype information:

Note: This is a comma-delimited file, in which the genotypes of diploid markers are represented by '.A' and '.B' as in the example file.

2. [Optional] Upload the file specifying parent genders or families ( Gender Family ):

Note: The "Gender file" (example) is a TAB-delimited file with one column specifying the gender ("female" or "male") of parents in a random mating population; and the "Family file" (example) is TAB-delimited file where each row stands for one family.

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3. Specify the algorithm:

Recommended Exhaustive Greedy

Greedy

Expected number of PMSs :

Maximum number of runs allowed for one PMS :

Markers to be excluded for subsequent PMSs :

all first marker(s)

Exhaustive

Minimum number of markers in a PMS :

Maximum number of markers in a PMS :

Note: 1. The maximum number of candidate markers and families are 10000 and 100, respectively. For this, the greedy algorithm is applied first, and if applicable (number of families does not exceed 17 and no more than 20 markers were obtained), the exhaustive algorithm is subsequently performed to refine the PMS; otherwise, the greedy algorithm will be performed solely.

Note: 1. Maximum number of candidate markers and families are 20 and 17, respectively.

Note: 1. Maximum number of candidate markers and families are 10000 and 100, respectively.

2.In case of systematic errors, we suggest the users to resubmit the task or contact us if the running takes 5,000 s or longer.

4. [Required] The email for receiving results :