(Q42281192)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28974235%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

review article

0 references

title

Alignment-free sequence comparison: benefits, applications, and tools (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28974235%20AND%20SRC:MED&resulttype=core&format=json

biomedical investigative technique

31 March 2020

main subject

1 reference

19 September 2019

1 reference

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28974235%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

Wojciech Karlowski

series ordinal

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28974235%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

3

Jonas Almeida

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28974235%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

author name string

Susana Vinga

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28974235%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

language of work or name

1 reference

3 October 2017

2 references

19 September 2019

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28974235%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

2 references

19 September 2019

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28974235%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

volume

18

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28974235%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

issue

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28974235%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

page(s)

186

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28974235%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

31 March 2020

copyright license

1 reference

https://scigraph.springernature.com/pub.10.1186/s13059-017-1319-7

19 September 2019

0 references

0 references

cites work

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26 October 2017

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StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees

26 October 2017

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Benchmarking of RNA-sequencing analysis workflows using whole-transcriptome RT-qPCR expression data

26 October 2017

1 reference

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ChimeRScope: a novel alignment-free algorithm for fusion transcript prediction using paired-end RNA-Seq data

26 October 2017

1 reference

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A coevolution analysis for identifying protein-protein interactions by Fourier transform

26 October 2017

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DLTree: efficient and accurate phylogeny reconstruction using the dynamical language method

26 October 2017

1 reference

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Comprehensive evaluation of RNA-seq quantification methods for linearity

26 October 2017

1 reference

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An accurate and fast alignment-free method for profiling microbial communities

26 October 2017

1 reference

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Salmon provides fast and bias-aware quantification of transcript expression

26 October 2017

1 reference

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Robust Inference of Genetic Exchange Communities from Microbial Genomes Using TF-IDF.

26 October 2017

1 reference

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Recapitulating phylogenies using k-mers: from trees to networks

26 October 2017

1 reference

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The super-n-motifs model: a novel alignment-free approach for representing and comparing RNA secondary structures

26 October 2017

1 reference

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Fast and accurate phylogeny reconstruction using filtered spaced-word matches.

26 October 2017

1 reference

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FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome

26 October 2017

1 reference

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MICADo - Looking for Mutations in Targeted PacBio Cancer Data: An Alignment-Free Method

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Zika and Flaviviruses Phylogeny Based on the Alignment-Free Natural Vector Method

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Alignment-free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

lncScore: alignment-free identification of long noncoding RNA from assembled novel transcripts

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Predictive computational phenotyping and biomarker discovery using reference-free genome comparisons.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

stringMLST: a fast k-mer based tool for multilocus sequence typing

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Fast genotyping of known SNPs through approximate k-mer matching

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Higher classification sensitivity of short metagenomic reads with CLARK-S.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

A novel alignment-free method for detection of lateral genetic transfer based on TF-IDF.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Mash: fast genome and metagenome distance estimation using MinHash

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

MetaFast: fast reference-free graph-based comparison of shotgun metagenomic data

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

MissMax: alignment-free sequence comparison with mismatches through filtering and heuristics

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Near-optimal probabilistic RNA-seq quantification

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

An evaluation of the accuracy and speed of metagenome analysis tools

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Multiple sequence alignment modeling: methods and applications

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Inference of Markovian properties of molecular sequences from NGS data and applications to comparative genomics.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

QuorUM: An Error Corrector for Illumina Reads

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

An alignment-free method to find and visualise rearrangements between pairs of DNA sequences

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

A statistical physics perspective on alignment-independent protein sequence comparison

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Clustering of reads with alignment-free measures and quality values

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Phy-Mer: a novel alignment-free and reference-independent mitochondrial haplogroup classifier.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

andi: fast and accurate estimation of evolutionary distances between closely related genomes

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Lighter: fast and memory-efficient sequencing error correction without counting

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Alignathon: a competitive assessment of whole-genome alignment methods

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Inferring phylogenies of evolving sequences without multiple sequence alignment.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

COMET: adaptive context-based modeling for ultrafast HIV-1 subtype identification.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

RNA-Skim: a rapid method for RNA-Seq quantification at transcript level

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

QMachine: commodity supercomputing in web browsers

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Kmacs: the k-mismatch average common substring approach to alignment-free sequence comparison

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Kraken: ultrafast metagenomic sequence classification using exact alignments

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Comparison of metatranscriptomic samples based on k-tuple frequencies

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

When whole-genome alignments just won't work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Compressive biological sequence analysis and archival in the era of high-throughput sequencing technologies

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

SCOPe: Structural Classification of Proteins--extended, integrating SCOP and ASTRAL data and classification of new structures

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Alignment-free phylogenetics and population genetics

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Pfam: the protein families database

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Applications of alignment-free methods in epigenomics

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Sequence analysis by iterated maps, a review

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Pattern recognition and probabilistic measures in alignment-free sequence analysis

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

An alignment-free test for recombination

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Information theory applications for biological sequence analysis

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Centroid based clustering of high throughput sequencing reads based on n-mer counts

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Multiple alignment-free sequence comparison

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

kClust: fast and sensitive clustering of large protein sequence databases

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Scalable metagenomic taxonomy classification using a reference genome database

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Alignment-free analysis of barcode sequences by means of compression-based methods

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Alignment-free sequence comparison based on next-generation sequencing reads

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Large local analysis of the unaligned genome and its application

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Comparison of metagenomic samples using sequence signatures

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Alignment-free phylogeny of whole genomes using underlying subwords

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

A hybrid distance measure for clustering expressed sequence tags originating from the same gene family

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

A phylogenetic analysis of the brassicales clade based on an alignment-free sequence comparison method

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

A novel hierarchical clustering algorithm for gene sequences

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Fractal MapReduce decomposition of sequence alignment

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Phylo: a citizen science approach for improving multiple sequence alignment

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

PTIGS-IdIt, a system for species identification by DNA sequences of the psbA-trnH intergenic spacer region

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Alignment-free detection of horizontal gene transfer between closely related bacterial genomes

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

2011 German Escherichia coli O104:H4 outbreak: whole-genome phylogeny without alignment.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

DNA barcode sequence identification incorporating taxonomic hierarchy and within taxon variability

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

New powerful statistics for alignment-free sequence comparison under a pattern transfer model

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs)

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Alignment-free detection of local similarity among viral and bacterial genomes

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Mugsy: fast multiple alignment of closely related whole genomes

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

A Clustering Optimization Strategy for Molecular Taxonomy Applied to Planktonic Foraminifera SSU rDNA

26 October 2017

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

26 October 2017

https://api.crossref.org/works/10.1186%2FS13059-017-1319-7

Classification of protein kinases on the basis of both kinase and non-kinase regions

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Clustering of protein families into functional subtypes using Relative Complexity Measure with reduced amino acid alphabets

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Quantifying the relationship between sequence and three-dimensional structure conservation in RNA.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Composition vector approach to whole-genome-based prokaryotic phylogeny: success and foundations

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Alignment-free sequence comparison (I): statistics and power

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Efficient alignment-free DNA barcode analytics

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Whole-genome phylogeny of mammals: evolutionary information in genic and nongenic regions

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Estimating mutation distances from unaligned genomes

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

A fungal phylogeny based on 82 complete genomes using the composition vector method

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

The Sequence Alignment/Map format and SAMtools

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Pattern-based phylogenetic distance estimation and tree reconstruction.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

On finding minimal absent words.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

BLOSUM62 miscalculations improve search performance

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Rates of evolutionary change in viruses: patterns and determinants

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Measuring the accuracy of genome-size multiple alignments

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Is multiple-sequence alignment required for accurate inference of phylogeny?

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Chaos game representation for comparison of whole genomes

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

The average common substring approach to phylogenomic reconstruction

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Genome comparison without alignment using shortest unique substrings

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

A benchmark of multiple sequence alignment programs upon structural RNAs

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Detection and characterization of horizontal transfers in prokaryotes using genomic signature

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Where did the BLOSUM62 alignment score matrix come from?

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Mauve: multiple alignment of conserved genomic sequence with rearrangements

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

CVTree: a phylogenetic tree reconstruction tool based on whole genomes

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Aligning multiple genomic sequences with the threaded blockset aligner

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

MUSCLE: multiple sequence alignment with high accuracy and high throughput

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Comparative evaluation of word composition distances for the recognition of SCOP relationships.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

A new sequence distance measure for phylogenetic tree construction

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Alignment-free sequence comparison-a review

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Human-mouse alignments with BLASTZ

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Genome rearrangements in mammalian evolution: lessons from human and mouse genomes

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

PipMaker--a web server for aligning two genomic DNA sequences

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

d2_cluster: a validated method for clustering EST and full-length cDNAsequences

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Genomic signature: characterization and classification of species assessed by chaos game representation of sequences

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Twilight zone of protein sequence alignments

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Biological evaluation of d2, an algorithm for high-performance sequence comparison.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

A measure of the similarity of sets of sequences not requiring sequence alignment

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Improved tools for biological sequence comparison

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Chaos game representation of gene structure

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Trowel: a fast and accurate error correction module for Illumina sequencing reads

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

A visual framework for sequence analysis using n-grams and spectral rearrangement

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Alignment uncertainty and genomic analysis

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Optimal word sizes for dissimilarity measures and estimation of the degree of dissimilarity between DNA sequences

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

ALFRED: A Practical Method for Alignment-Free Distance Computation.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Alignment-free comparison of genome sequences by a new numerical characterization

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

An alignment-free model for comparison of regulatory sequences

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Markov model plus k-word distributions: a synergy that produces novel statistical measures for sequence comparison

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

A statistical method for alignment-free comparison of regulatory sequences.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Identifying candidate subunit vaccines using an alignment-independent method based on principal amino acid properties.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Metrics for comparing regulatory sequences on the basis of pattern counts.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

A measure of DNA sequence dissimilarity based on Mahalanobis distance between frequencies of words.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

What is dynamic programming?

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5627421

An Introduction to Kolmogorov Complexity and Its Applications

30 September 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-017-1319-7

21 January 2018

Energy and Information

1 reference

https://api.crossref.org/works/10.1186%2FS13059-017-1319-7

On Information and Sufficiency

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-017-1319-7

Bioinformatics tools for predicting GPCR gene functions

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-017-1319-7

CAFE: aCcelerated Alignment-FrEe sequence analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-017-1319-7

Update: transmission of HIV infection during invasive dental procedures--Florida

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28974235

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Editorial: Alignment-free methods in computational biology

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28974235

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Microbiology by numbers

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28974235

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/S13059-017-1319-7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28974235%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

31 March 2020

1 reference

9 September 2019

https://scigraph.springernature.com/pub.10.1186/s13059-017-1319-7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28974235%20AND%20SRC:MED&resulttype=core&format=json

31 March 2020

PubMed publication ID

28974235

1 reference