Back

REDigest: a Python GUI for In-Silico Restriction Digestion Analysis of Genes or Complete Genome Sequences

Singh, A.

2021-11-11 bioinformatics
10.1101/2021.11.09.467873 bioRxiv
Show abstract

Restriction fragment length polymorphism (RFLP) is a technology for the molecular characterization of DNA and widely used genome mapping, medical genetics, molecular microbiology and forensics etc. Terminal restriction fragment length polymorphism (T-RFLP), a variant of RFLP is extensively used in environmental microbiology for the microbial community profiling based on the restriction digestion profile of marker gene (16S rRNA, FTHFS etc.) amplicons. At present, there is a lack of a tool which can perform in-silico restriction digestion of a large number of sequences at a time, in an interactive way and as an output produce sequences of the restriction fragments and visualization plot. I have developed a graphical user interface based software "REDigest" for the in-silico restriction digestion analysis for gene or genome sequences. The REDigest software program with a graphical user interface is freely available at https://github.com/abhijeetsingh1704/REDigest.

Matching journals

The top 6 journals account for 50% of the predicted probability mass.

1
BMC Bioinformatics
○ 457 papers in training set
Top 0.4%
12.8%
Similar papers in this journal
2
PLOS ONE
● 5266 papers in training set
Top 15%
12.1%
Similar papers in this journal
3
PeerJ
◐ 308 papers in training set
Top 0.2%
9.8%
Similar papers in this journal
4
F1000Research
○ 88 papers in training set
Top 0.1%
6.8%
Similar papers in this journal
5
Bioinformatics
◐ 1204 papers in training set
Top 4%
6.3%
Similar papers in this journal
6
Gigabyte
● 62 papers in training set
Top 0.3%
3.2%
50% of probability mass above
7
Journal of Bioinformatics and Systems Biology
○ 15 papers in training set
Top 0.1%
2.7%
8
Bioinformatics Advances
◐ 203 papers in training set
Top 2%
2.7%
9
Scientific Reports
○ 3612 papers in training set
Top 41%
2.4%
10
Genes
○ 144 papers in training set
Top 1%
2.1%
11
Briefings in Bioinformatics
◐ 354 papers in training set
Top 4%
2.1%
12
BMC Genomics
○ 406 papers in training set
Top 3%
2.1%
13
GigaScience
◐ 212 papers in training set
Top 2%
1.8%
14
Genomics
○ 64 papers in training set
Top 0.8%
1.7%
15
Frontiers in Microbiology
○ 427 papers in training set
Top 6%
1.4%
16
Biology
○ 45 papers in training set
Top 0.3%
1.1%
17
BMC Research Notes
○ 33 papers in training set
Top 0.7%
1.1%
18
Computational Biology and Chemistry
○ 28 papers in training set
Top 0.8%
1.1%
19
Peer Community Journal
● 281 papers in training set
Top 4%
1.0%
20
Plant Methods
○ 42 papers in training set
Top 0.7%
0.9%
21
Frontiers in Genetics
○ 230 papers in training set
Top 5%
0.9%
22
Database
◐ 61 papers in training set
Top 0.9%
0.9%
23
Computational and Structural Biotechnology Journal
● 242 papers in training set
Top 6%
0.9%
24
Biology Methods and Protocols
◐ 61 papers in training set
Top 2%
0.9%
25
Genomics, Proteomics & Bioinformatics
188 papers in training set
Top 2%
0.6%
26
Applied Microbiology and Biotechnology
○ 32 papers in training set
Top 0.9%
0.6%
27
Biochimie
○ 25 papers in training set
Top 0.9%
0.6%
28
SoftwareX
○ 15 papers in training set
Top 0.3%
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.