Back

Bi-Alignments as Models of Incongruent Evolution of RNA Sequence and Structure

Waldl, M.; Will, S.; Wolfinger, M. T.; Hofacker, I. L.; Stadler, P. F.

2019-07-29 bioinformatics
10.1101/631606 bioRxiv
Show abstract

RNA molecules may experience independent selection pressures on their sequence and (secondary) structure. Structural features then may be preserved without maintaining their exact position along the sequence. In such cases, corresponding base pairs are no longer formed by homologous bases, leading to the incongruent evolutionary conservation of sequence and structure. In order to model this phenomenon, we introduce bi-alignments as a superposition of two alignments: one modeling sequence homology; the other, structural homology. We show that under natural assumptions on the scoring functions, bi-alignments form a special case of 4-way alignments, in which the incongruencies are measured as indels in the pairwise alignment of the two alignment copies. A preliminary survey of the Rfam database suggests that incongruent evolution of RNAs is not a very rare phenomenon.\n\nAvailabilityOur software is freely available at https://github.com/s-will/BiAlign

Matching journals

The top 5 journals account for 50% of the predicted probability mass.

1
Bioinformatics
◐ 1204 papers in training set
Top 0.9%
22.6%
Similar papers in this journal
2
Algorithms for Molecular Biology
○ 17 papers in training set
Top 0.1%
11.1%
Similar papers in this journal
3
Journal of Computational Biology
○ 48 papers in training set
Top 0.1%
8.0%
Similar papers in this journal
4
PLOS Computational Biology
● 1863 papers in training set
Top 4%
8.0%
Similar papers in this journal
5
BMC Bioinformatics
○ 457 papers in training set
Top 1%
7.3%
Similar papers in this journal
50% of probability mass above
6
RNA
● 189 papers in training set
Top 0.3%
6.8%
7
Bioinformatics Advances
◐ 203 papers in training set
Top 2%
3.3%
8
NAR Genomics and Bioinformatics
◐ 242 papers in training set
Top 1%
3.3%
9
Cell Systems
○ 201 papers in training set
Top 2%
2.5%
10
PeerJ
◐ 308 papers in training set
Top 4%
2.1%
11
Genome Research
● 468 papers in training set
Top 3%
2.1%
12
Nature Communications
○ 5641 papers in training set
Top 44%
1.7%
13
Scientific Reports
○ 3612 papers in training set
Top 51%
1.7%
14
PLOS ONE
● 5266 papers in training set
Top 48%
1.5%
15
Molecular Biology and Evolution
◐ 542 papers in training set
Top 4%
1.4%
16
IEEE/ACM Transactions on Computational Biology and Bioinformatics
● 38 papers in training set
Top 0.8%
1.1%
17
Nucleic Acids Research
◐ 1281 papers in training set
Top 12%
1.0%
18
Genome Biology
○ 637 papers in training set
Top 8%
0.9%
19
Nature Methods
○ 385 papers in training set
Top 6%
0.9%
20
F1000Research
○ 88 papers in training set
Top 4%
0.6%
21
Systematic Biology
◐ 144 papers in training set
Top 0.8%
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.