Sequence context-specific profiles for homology searching (Q24650356)

https://www.ncbi.nlm.nih.gov/pubmed/19234132

15 May 2017

BLAST

1 reference

https://www.ncbi.nlm.nih.gov/pubmed/19234132

15 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

Recent evolutions of multiple sequence alignment algorithms

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

Contextual multiple sequence alignment

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

TM-align: a protein structure alignment algorithm based on the TM-score

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

EvDTree: structure-dependent substitution profiles based on decision tree classification of 3D environments

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

Profile analysis: detection of distantly related proteins

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

Amino acid substitution matrices from protein blocks

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

Basic local alignment search tool

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

Profile hidden Markov models

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

Mapping the protein universe

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

SCOP: a structural classification of proteins database for the investigation of sequences and structures

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

Identification of common molecular subsequences

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

A general method applicable to the search for similarities in the amino acid sequence of two proteins

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

Protein homology detection by HMM-HMM comparison

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

Exhaustive matching of the entire protein sequence database

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

Profile Comparer: a program for scoring and aligning profile hidden Markov models

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

Context-specific amino acid substitution matrices and their use in the detection of protein homologs

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

The compositional adjustment of amino acid substitution matrices

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

Non-symmetric score matrices and the detection of homologous transmembrane proteins

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

Use of residue pairs in protein sequence-sequence and sequence-structure alignments

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

Global properties of the mapping between local amino acid sequence and local structure in proteins

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

A mutation data matrix for transmembrane proteins

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

Amino acid substitution matrices from an information theoretic perspective

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

Pairwise alignment incorporating dipeptide covariation.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

Comparison of sequence profiles. Strategies for structural predictions using sequence information

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

PHAT: a transmembrane-specific substitution matrix. Predicted hydrophobic and transmembrane

30 May 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0810767106

Periodic distributions of hydrophobic amino acids allows the definition of fundamental building blocks to align distantly related proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0810767106

Within the twilight zone: a sensitive profile-profile comparison tool based on information theory.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0810767106

SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0810767106

Contextual alignment of biological sequences (Extended abstract).

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2645910

Using substitution probabilities to improve position-specific scoring matrices

28 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19234132

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19234132

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.0810767106

1 reference

1524240

ADS bibcode

2009PNAS..106.3770B

0 references

1524240

1 reference

1 reference

1 reference