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_Residue
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
(?)
Feature selection
(?)
mutual information
chi-square
Dimensions
(?)
2000
1000
500
400
300
200
100
50
Fragment
(?)
No
Yes
Window size
(?)
Type of problem
(?)
Binary classification
Multiclass classification
Number of labels
(?)
2
3
4
5
6
Machine learning algorithm
(?)
Support Vector Machine
Random Forest
Conditional Random Field
Parameter optimization
(?)
No
Yes
C(cost)
(?)
2⁻¹
2⁰
2¹
2²
2³
2⁴
2⁵
2⁶
2⁷
From:
2⁻¹
2⁰
2¹
To:
2⁵
2⁷
g(gamma)
(?)
2⁻⁷
2⁻⁶
2⁻⁵
2⁻⁴
2⁻³
2⁻²
2⁻¹
2⁰
2¹
2²
2³
From:
2⁻⁷
2⁻⁵
2⁻³
To:
2⁻¹
2⁰
2³
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
Cross validation
(?)
5-fold cross validation
Independent dataset test
Input the independent dataset in FASTA format
(?)
:
(minimum 5 sequences for each submission)
or upload a file in FASTA format
(?)
:
Labels of independent dataset
(?)
:
Input your e-mail(optional)
(?)
Sequence Input:
Input DNA sequences in FASTA format
(?)
:
(5-100 sequences for each submission)
or upload a file in FASTA format
(?)
:
Label Input:
Input the DNA sequences label in FASTA format
(?)
:
(each DNA residue must be aligned with the label)
or upload a file in FASTA format
(?)
:
Please wait.........
Copyright@ By Liu Lab, Beijing Institute of Technology.
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