Back

ePat: extended PROVEAN annotation tool

Ito, T.; Yoshitake, K.; Iwata, T.

2021-12-23 bioinformatics
10.1101/2021.12.21.468911 bioRxiv
Show abstract

The ePat (extended PROVEAN annotation tool) is a software tool that extends the functionality of PROVEAN: a software tool for predicting whether amino acid substitutions and indels will affect the biological function of proteins. The ePat extends the conventional PROVEAN to enable the following two things, which the conventional PROVEAN could not calculate the pathogenicity of these variants. First is to calculate and score the pathogenicity of indel mutations with frameshift and variants near splice junctions. Second is to use batch processing to calculate the pathogenicity of multiple variants into a variants list (VCF file) in a single step. ePat can help extract variants that affect biological functions by utilizing not only point mutations, and indel mutations that does not cause frameshift, but also frameshift, stop gain, and splice variants. These extended features will increase detection rate and improve diagnostic of inherited diseases or associate specific variant to phenotype.

Matching journals

The top 2 journals account for 50% of the predicted probability mass.

1
BMC Bioinformatics
○ 457 papers in training set
Top 0.1%
39.7%
2
Bioinformatics
◐ 1204 papers in training set
Top 2%
15.1%
50% of probability mass above
3
PLOS Computational Biology
● 1863 papers in training set
Top 8%
4.3%
4
PLOS ONE
● 5266 papers in training set
Top 35%
3.5%
5
Bioinformatics Advances
◐ 203 papers in training set
Top 2%
2.4%
6
IEEE/ACM Transactions on Computational Biology and Bioinformatics
● 38 papers in training set
Top 0.4%
2.4%
7
Database
◐ 61 papers in training set
Top 0.3%
2.4%
8
NAR Genomics and Bioinformatics
◐ 242 papers in training set
Top 2%
2.4%
9
Human Mutation
○ 34 papers in training set
Top 0.3%
2.0%
10
Nucleic Acids Research
◐ 1281 papers in training set
Top 8%
1.9%
11
Journal of Bioinformatics and Systems Biology
○ 15 papers in training set
Top 0.1%
1.7%
12
Genes
○ 144 papers in training set
Top 2%
1.7%
13
BMC Genomics
○ 406 papers in training set
Top 5%
1.5%
14
F1000Research
○ 88 papers in training set
Top 2%
1.4%
15
Informatics in Medicine Unlocked
○ 22 papers in training set
Top 0.9%
1.1%
16
GigaScience
◐ 212 papers in training set
Top 3%
1.1%
17
BMC Medical Genomics
○ 50 papers in training set
Top 0.8%
1.1%
18
Gigabyte
● 62 papers in training set
Top 1.0%
1.0%
19
Scientific Reports
○ 3612 papers in training set
Top 71%
1.0%
20
BioData Mining
○ 22 papers in training set
Top 0.8%
0.8%
21
Briefings in Bioinformatics
◐ 354 papers in training set
Top 7%
0.8%
22
Frontiers in Genetics
○ 230 papers in training set
Top 7%
0.6%
23
PeerJ
◐ 308 papers in training set
Top 13%
0.6%
24
Computational and Structural Biotechnology Journal
● 242 papers in training set
Top 8%
0.6%