Back

IIIandMe: An Algorithm for Chromosome-scale Haplotype Determination Using Genome-wide Variants of Three Haploid Reproductive Cells

Jia, Z.; Qu, H.; Li, R.

2022-12-12 bioinformatics
10.1101/2022.12.07.519546 bioRxiv
Show abstract

Our recent algorithm, Hapi, infers chromosome-scale haplotypes using genomic data of a small number of single gametes. Its advanced version, IIIandMe, is proposed here to achieve comparable phasing accuracy with as few as three gametes, pushing the analysis to its limit. The new method is validated with simulation and a citrus gamete dataset. The rapid advances in genotyping technologies promise a broad application of IIIandMe in disclosing important genetic information.

Matching journals

The top 7 journals account for 50% of the predicted probability mass.

1
Bioinformatics
◐ 1204 papers in training set
Top 1%
18.6%
Similar papers in this journal
2
PLOS Computational Biology
● 1863 papers in training set
Top 3%
9.9%
Similar papers in this journal
3
Genome Research
● 468 papers in training set
Top 0.9%
6.3%
Similar papers in this journal
4
BMC Genomics
○ 406 papers in training set
Top 1%
4.9%
5
BMC Bioinformatics
○ 457 papers in training set
Top 2%
4.9%
Similar papers in this journal
6
GENETICS
◐ 483 papers in training set
Top 1%
4.9%
Similar papers in this journal
7
Theoretical and Applied Genetics
○ 49 papers in training set
Top 0.3%
4.1%
50% of probability mass above
8
Briefings in Bioinformatics
◐ 354 papers in training set
Top 3%
3.2%
9
Molecular Biology and Evolution
◐ 542 papers in training set
Top 3%
2.5%
10
G3: Genes, Genomes, Genetics
◐ 252 papers in training set
Top 2%
2.5%
11
Bioinformatics Advances
◐ 203 papers in training set
Top 3%
2.1%
12
G3 Genes|Genomes|Genetics
◐ 351 papers in training set
Top 2%
2.1%
13
Nucleic Acids Research
◐ 1281 papers in training set
Top 8%
1.7%
14
Molecular Ecology Resources
○ 171 papers in training set
Top 1%
1.7%
15
Genome Biology
○ 637 papers in training set
Top 6%
1.7%
16
The Plant Journal
○ 215 papers in training set
Top 2%
1.7%
17
The Plant Genome
○ 57 papers in training set
Top 0.6%
1.5%
18
Frontiers in Genetics
○ 230 papers in training set
Top 3%
1.5%
19
iScience
○ 1154 papers in training set
Top 22%
1.4%
20
eLife
● 5828 papers in training set
Top 56%
1.3%
21
Horticulture Research
◐ 47 papers in training set
Top 0.6%
1.3%
22
Scientific Reports
○ 3612 papers in training set
Top 59%
1.3%
23
PLOS ONE
● 5266 papers in training set
Top 52%
1.1%
24
Frontiers in Plant Science
○ 256 papers in training set
Top 4%
1.1%
25
Nature Communications
○ 5641 papers in training set
Top 52%
1.1%
26
PLOS Genetics
● 862 papers in training set
Top 10%
1.1%
27
NAR Genomics and Bioinformatics
◐ 242 papers in training set
Top 4%
1.0%
28
IEEE Transactions on Computational Biology and Bioinformatics
● 20 papers in training set
Top 0.7%
0.6%
29
Plant Physiology
◐ 238 papers in training set
Top 3%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.