BioSeq-Analysis: a platform for DNA, RNA and protein sequence analysis based on machine learning approaches (Q47173127)

11 January 2018

title

BioSeq-Analysis: a platform for DNA, RNA and protein sequence analysis based on machine learning approaches (English)

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11 January 2018

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1 reference

Bin Liu

1

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11 January 2018

publication date

19 December 2017

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11 January 2018

Briefings in Bioinformatics

published in

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11 January 2018

The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.

volume

20

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page(s)

1280-1294

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issue

4

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cites work

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

21 January 2018

The Protein Data Bank

1 reference

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Identification of real microRNA precursors with a pseudo structure status composition approach

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

iEnhancer-2L: a two-layer predictor for identifying enhancers and their strength by pseudo k-tuple nucleotide composition

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Protein fold recognition based on sparse representation based classification

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

ProtDec-LTR2.0: an improved method for protein remote homology detection by combining pseudo protein and supervised Learning to Rank.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Recombination spot identification Based on gapped k-mers

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

A comprehensive comparative review of sequence-based predictors of DNA- and RNA-binding residues.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

PSFM-DBT: Identifying DNA-Binding Proteins by Combing Position Specific Frequency Matrix and Distance-Bigram Transformation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Pattern recognition in bioinformatics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Combining evolutionary information and neural networks to predict protein secondary structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

iDHS-EL: identifying DNase I hypersensitive sites by fusing three different modes of pseudo nucleotide composition into an ensemble learning framework

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Predicting human nucleosome occupancy from primary sequence

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

The organization of nucleosomes around splice sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Sequence-dependent prediction of recombination hotspots in Saccharomyces cerevisiae.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Splice site prediction with quadratic discriminant analysis using diversity measure

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Prediction for human transcription start site using diversity measure with quadratic discriminant

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Accurate Prediction of Transposon-Derived piRNAs by Integrating Various Sequential and Physicochemical Features

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Mismatch string kernels for discriminative protein classification

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

iRSpot-DACC: a computational predictor for recombination hot/cold spots identification based on dinucleotide-based auto-cross covariance

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

A new taxonomy-based protein fold recognition approach based on autocross-covariance transformation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

iMiRNA-SSF: Improving the Identification of MicroRNA Precursors by Combining Negative Sets with Different Distributions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

iRNA-Methyl: Identifying N(6)-methyladenosine sites using pseudo nucleotide composition.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Vienna RNA secondary structure server

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

iMiRNA-PseDPC: microRNA precursor identification with a pseudo distance-pair composition approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Identification of microRNA precursor with the degenerate K-tuple or Kmer strategy

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

A discriminative method for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Using amino acid physicochemical distance transformation for fast protein remote homology detection

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Physicochemical property distributions for accurate and rapid pairwise protein homology detection

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Prediction of protein cellular attributes using pseudo-amino acid composition

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Some remarks on protein attribute prediction and pseudo amino acid composition

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

PseDNA-Pro: DNA-Binding Protein Identification by Combining Chou's PseAAC and Physicochemical Distance Transformation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Profile-based direct kernels for remote homology detection and fold recognition.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Prediction of protein binding sites in protein structures using hidden Markov support vector machine

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Application of multiple sequence alignment profiles to improve protein secondary structure prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Protein-protein interaction site prediction based on conditional random fields.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Predicting eukaryotic protein subcellular location by fusing optimized evidence-theoretic K-Nearest Neighbor classifiers

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

The use of classification trees for bioinformatics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Identification of DNA-binding proteins by combining auto-cross covariance transformation and ensemble learning.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

2L-piRNA: A Two-Layer Ensemble Classifier for Identifying Piwi-Interacting RNAs and Their Function

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

iRSpot-EL: identify recombination spots with an ensemble learning approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Ensemble classifier for protein fold pattern recognition.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

repDNA: a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

PseKNC: a flexible web server for generating pseudo K-tuple nucleotide composition.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

PseKNC-General: a cross-platform package for generating various modes of pseudo nucleotide compositions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

repRNA: a web server for generating various feature vectors of RNA sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

PseAAC: a flexible web server for generating various kinds of protein pseudo amino acid composition

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

propy: a tool to generate various modes of Chou's PseAAC.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

PseAAC-Builder: a cross-platform stand-alone program for generating various special Chou's pseudo-amino acid compositions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Predicting effects of noncoding variants with deep learning-based sequence model

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Protein remote homology detection based on bidirectional long short-term memory

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Prediction of membrane protein types based on the hydrophobic index of amino acids

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Improved and Promising Identification of Human MicroRNAs by Incorporating a High-Quality Negative Set.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

iDNA-Prot|dis: identifying DNA-binding proteins by incorporating amino acid distance-pairs and reduced alphabet profile into the general pseudo amino acid composition

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

EL_PSSM-RT: DNA-binding residue prediction by integrating ensemble learning with PSSM Relation Transformation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Mutual information between discrete and continuous data sets

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

21 January 2018

Support-vector networks

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

pSumo-CD: predicting sumoylation sites in proteins with covariance discriminant algorithm by incorporating sequence-coupled effects into general PseAAC.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

An introduction to ROC analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

iHSP-PseRAAAC: Identifying the heat shock protein families using pseudo reduced amino acid alphabet composition

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Selecting and interpreting measures of thematic classification accuracy

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

The chromatin structure of specific genes: I. Evidence for higher order domains of defined DNA sequence

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

DNA binding protein identification by combining pseudo amino acid composition and profile-based protein representation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBX165

Protein Remote Homology Detection by Combining Chou's Pseudo Amino Acid Composition and Profile-Based Protein Representation

21 January 2018

1 reference

COCI

https://opencitations.net/index/coci/api/v1/citations/10.1002/MINF.201300084

8 April 2023

Identifiers

DOI

10.1093/BIB/BBX165

1 reference

11 January 2018

DBLP publication ID

journals/bib/Liu19

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

11 January 2018