(Q39017728)

8 September 2017

Protein multiple sequence alignment benchmarking through secondary structure prediction (English)

1 reference

protein structure prediction

8 September 2017

0 references

1 reference

Quan Le

1

1 reference

8 September 2017

Fabian Sievers

series ordinal

2

1 reference

8 September 2017

Desmond G Higgins

series ordinal

3

1 reference

8 September 2017

language of work or name

English

0 references

publication date

16 January 2017

1 reference

8 September 2017

1 reference

8 September 2017

33

1 reference

8 September 2017

9

1 reference

8 September 2017

1331-1337

1 reference

Creative Commons Attribution 4.0 International

8 September 2017

start time

16 January 2017

1 reference

April 2023 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Reduction, alignment and visualisation of large diverse sequence families

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

Multiple sequence alignment modeling: methods and applications

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

Using de novo protein structure predictions to measure the quality of very large multiple sequence alignments.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

JPred4: a protein secondary structure prediction server

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

Pfam: the protein families database

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

Protein structure prediction from sequence variation

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

Advances and pitfalls of protein structural alignment

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

Clustal W and Clustal X version 2.0

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

Kalign--an accurate and fast multiple sequence alignment algorithm

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

Porter: a new, accurate server for protein secondary structure prediction

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

CE-MC: a multiple protein structure alignment server.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

MUSCLE: multiple sequence alignment with high accuracy and high throughput

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

T-Coffee: A novel method for fast and accurate multiple sequence alignment

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

Protein secondary structure prediction based on position-specific scoring matrices

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

A comprehensive comparison of multiple sequence alignment programs

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

Profile hidden Markov models

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

HOMSTRAD: a database of protein structure alignments for homologous families

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

Multiple protein structure alignment

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

Quality measures for protein alignment benchmarks

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

Phylogenetic assessment of alignments reveals neglected tree signal in gaps

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

Sequence embedding for fast construction of guide trees for multiple sequence alignment

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

MUSTANG: a multiple structural alignment algorithm.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

Reply to Tan et al.: Differences between real and simulated proteins in multiple sequence alignments

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

Making automated multiple alignments of very large numbers of protein sequences

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5408826

10.1093/BIOINFORMATICS/BTW840

21 August 2018

Identifiers

DOI

1 reference

journals/bioinformatics/LeSH17

8 September 2017

1 reference

DBLP Dataset 2021-01-02

release_vgnxnvmqzbhsxlkrd47ppliw5e

28 January 2021

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/vgnxnvmqzbhsxlkrd47ppliw5e

mapped directly with Wikidata item

24 November 2022

based on heuristic

1 reference

8 September 2017

PubMed publication ID

28093407

1 reference