PSimScan: algorithm and utility for fast protein similarity search (Q34625877)

3 August 2017

title

PSimScan: algorithm and utility for fast protein similarity search (English)

1 reference

3 August 2017

Anna Kaznadzey

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Natalia Alexandrova

1 reference

3 August 2017

Vladimir Novichkov

series ordinal

1 reference

3 August 2017

Denis Kaznadzey

series ordinal

1 reference

3 August 2017

language of work or name

English

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publication date

7 March 2013

1 reference

3 August 2017

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3 August 2017

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3 August 2017

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3 August 2017

page(s)

e58505

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Creative Commons CC0 License

3 August 2017

start time

7 March 2013

1 reference

April 2022 Public Data File from Crossref

copyrighted, dedicated to the public domain by copyright holder

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cites work

Accelerated Profile HMM Searches

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

RAPSearch: a fast protein similarity search tool for short reads

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

On the Future of Genomic Data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

Hidden Markov model speed heuristic and iterative HMM search procedure

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

Search and clustering orders of magnitude faster than BLAST

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

A survey of sequence alignment algorithms for next-generation sequencing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

A new generation of homology search tools based on probabilistic inference

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

Sequence context-specific profiles for homology searching

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

MaxAlign: maximizing usable data in an alignment

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

Clustered sequence representation for fast homology search

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

Fast model-based protein homology detection without alignment

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

PHOG-BLAST--a new generation tool for fast similarity search of protein families

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

The ASTRAL Compendium in 2004

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

BLAT—The BLAST-Like Alignment Tool

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

Flexible sequence similarity searching with the FASTA3 program package

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

Profile hidden Markov models

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

Protein sequence similarity searches using patterns as seeds

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

Generalized affine gap costs for protein sequence alignment

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

A protein alignment scoring system sensitive at all evolutionary distances

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

Identification of common molecular subsequences

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

Improved tools for biological sequence comparison

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

Rapid and sensitive protein similarity searches

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

Basic local alignment search tool

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

Rapid and sensitive sequence comparison with FASTP and FASTA

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

Amino acid substitution matrices from protein blocks

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3591303

A deterministic finite automaton for faster protein hit detection in BLAST.

7 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0058505

Improved gapped alignment in BLAST.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0058505

Comparing compressed sequences for faster nucleotide BLAST searches.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0058505

Organizing and updating whole genome BLAST searches with ReHAB.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0058505

The efficient computation of position-specific match scores with the fast fourier transform

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0058505

Accurate formula for P-values of gapped local sequence and profile alignments

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23505522

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

BEAUTY: an enhanced BLAST-based search tool that integrates multiple biological information resources into sequence similarity search results

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23505522

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0058505

1 reference

3 August 2017

0 references

1 reference

3 August 2017

1 reference