BioSeq-Analysis2.0:an updated platform for analyzing DNA, RNA, and protein sequences at sequence level and residue level based on machine learning approaches
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DNA-Analysis2.0
RNA-Analysis2.0
Protein-Analysis2.0
DNA
Mode
(?)
----------------------------
** Residue-Level **
----------------------------
One-hot
Position-specific-2
Position-specific-3
Position-specific-4
DPC
TPC
BLAST-matrix
----------------------------
** Sequence-Level **
----------------------------
NAC
DNC
TNC
CKSNAP
NCP
ANF
EIIP
PseEIIP
Zcurve
Kmer
RevKmer
IDKmer
Mismatch
Subsequence
DAC
DCC
DACC
TAC
TCC
TACC
MAC
GAC
NMBAC
PseDNC
PseKNC
PC-PseDNC-General
PC-PseTNC-General
SC-PseDNC-General
SC-PseTNC-General
(?)
Parameter optimization
(?)
No
Yes
k
(?)
1
2
3
4
5
6
From:
1
2
To:
3
4
5
6
Enter the positive source data in FASTA format
(?)
:
or upload a file in FASTA format
(?)
:
Enter the negative source data in FASTA format
(?)
:
or upload a file in FASTA format
(?)
:
Feature selection
(?)
mutual information
chi-square
Dimensions
(?)
10000
5000
3000
1000
500
400
300
200
100
50
Type of problem
(?)
Binary classification
Multiclass classification
Number of class
(?)
3
4
5
6
Machine learning algorithm
(?)
Support Vector Machine
Random Forest
OET-KNN
Covariance Discriminant
Parameter optimization
(?)
No
Yes
C(cost)
(?)
2⁻¹
2⁰
2¹
2²
2³
2⁴
2⁵
From:
2⁻¹
2⁰
2¹
To:
2³
2⁴
2⁵
g(gamma)
(?)
2⁻⁵
2⁻⁴
2⁻³
2⁻²
2⁻¹
2⁰
2¹
2²
2³
From:
2⁻⁵
2⁻⁴
2⁻³
To:
2⁻¹
2⁰
2¹
n_estimators
(?)
50
100
200
300
400
500
From:
100
200
300
To:
400
500
600
neighbors
(?)
3
5
7
9
11
13
From:
3
5
7
To:
11
13
15
Performance measure for parameter optimization
(?)
ACC
MCC
AUC
Sampling
(?)
None
Under sampling
Oversampling
Cross validation
(?)
5-fold cross validation
Independent dataset test
Bootstrapping
Input the independent dataset in FASTA format
(?)
:
(5-600 sequences for each submission)
or upload a file in FASTA format
(?)
:
Labels of independent dataset
(?)
:
Input your e-mail(optional)
(?)
Input the positive query DNA sequences in FASTA format
(?)
:
(5-600 sequences for each submission)
or upload a file in FASTA format
(?)
:
Input the negative query DNA sequences in FASTA format
(?)
:
(5-600 sequences for each submission)
or upload a file in FASTA format
(?)
:
Please wait.........
Copyright@ By Liu Lab, Beijing Institute of Technology.
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