Warning: Undefined array key "mm" in /www/wwwroot/www.ai-bt.com/si.php on line 10 Deprecated: trim(): Passing null to parameter #1 ($string) of type string is deprecated in /www/wwwroot/www.ai-bt.com/si.php on line 10 HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment.

Literature DB >> 22198341

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment.

Michael Remmert¹, Andreas Biegert, Andreas Hauser, Johannes Söding.

Abstract

Sequence-based protein function and structure prediction depends crucially on sequence-search sensitivity and accuracy of the resulting sequence alignments. We present an open-source, general-purpose tool that represents both query and database sequences by profile hidden Markov models (HMMs): 'HMM-HMM-based lightning-fast iterative sequence search' (HHblits; http://toolkit.genzentrum.lmu.de/hhblits/). Compared to the sequence-search tool PSI-BLAST, HHblits is faster owing to its discretized-profile prefilter, has 50-100% higher sensitivity and generates more accurate alignments.

Mesh：

Substances：
Proteins

Year: 2011 PMID： 22198341 DOI： 10.1038/nmeth.1818

Source DB: PubMed Journal: Nat Methods ISSN： 1548-7091 Impact factor: 28.547

21 in total

1. Protein secondary structure prediction based on position-specific scoring matrices.

Authors: D T Jones
Journal: J Mol Biol Date: 1999-09-17 Impact factor: 5.469

2. Annotation transfer for genomics: measuring functional divergence in multi-domain proteins.

Authors: H Hegyi; M Gerstein
Journal: Genome Res Date: 2001-10 Impact factor: 9.043

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

Authors: Weizhong Li; Adam Godzik
Journal: Bioinformatics Date: 2006-05-26 Impact factor: 6.937

4. De novo identification of highly diverged protein repeats by probabilistic consistency.

Authors: A Biegert; J Söding
Journal: Bioinformatics Date: 2008-02-01 Impact factor: 6.937

5. Sequence context-specific profiles for homology searching.

Authors: A Biegert; J Söding
Journal: Proc Natl Acad Sci U S A Date: 2009-02-20 Impact factor: 11.205

6. A new generation of homology search tools based on probabilistic inference.

Authors: Sean R Eddy
Journal: Genome Inform Date: 2009-10

7. The Pfam protein families database.

Authors: Robert D Finn; Jaina Mistry; John Tate; Penny Coggill; Andreas Heger; Joanne E Pollington; O Luke Gavin; Prasad Gunasekaran; Goran Ceric; Kristoffer Forslund; Liisa Holm; Erik L L Sonnhammer; Sean R Eddy; Alex Bateman
Journal: Nucleic Acids Res Date: 2009-11-17 Impact factor: 16.971

8. PDBselect 1992-2009 and PDBfilter-select.

Authors: Sven Griep; Uwe Hobohm
Journal: Nucleic Acids Res Date: 2009-09-25 Impact factor: 16.971

9. Learning sparse models for a dynamic Bayesian network classifier of protein secondary structure.

Authors: Zafer Aydin; Ajit Singh; Jeff Bilmes; William S Noble
Journal: BMC Bioinformatics Date: 2011-05-13 Impact factor: 3.169

10. Data growth and its impact on the SCOP database: new developments.

Authors: Antonina Andreeva; Dave Howorth; John-Marc Chandonia; Steven E Brenner; Tim J P Hubbard; Cyrus Chothia; Alexey G Murzin
Journal: Nucleic Acids Res Date: 2007-11-13 Impact factor: 16.971

691 in total

1. Membrane protein structure predictions for exploration.

Authors: Nick V Grishin
Journal: Cell Date: 2012-06-22 Impact factor: 41.582

2. Unexpected features of the dark proteome.

Authors: Nelson Perdigão; Julian Heinrich; Christian Stolte; Kenneth S Sabir; Michael J Buckley; Bruce Tabor; Beth Signal; Brian S Gloss; Christopher J Hammang; Burkhard Rost; Andrea Schafferhans; Seán I O'Donoghue
Journal: Proc Natl Acad Sci U S A Date: 2015-11-17 Impact factor: 11.205

3. Analysis of 51 cyclodipeptide synthases reveals the basis for substrate specificity.

Authors: Isabelle B Jacques; Mireille Moutiez; Jerzy Witwinowski; Emmanuelle Darbon; Cécile Martel; Jérôme Seguin; Emmanuel Favry; Robert Thai; Alain Lecoq; Steven Dubois; Jean-Luc Pernodet; Muriel Gondry; Pascal Belin
Journal: Nat Chem Biol Date: 2015-08-03 Impact factor: 15.040

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment.

1. Protein secondary structure prediction based on position-specific scoring matrices.

2. Annotation transfer for genomics: measuring functional divergence in multi-domain proteins.

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

4. De novo identification of highly diverged protein repeats by probabilistic consistency.

5. Sequence context-specific profiles for homology searching.

6. A new generation of homology search tools based on probabilistic inference.

7. The Pfam protein families database.

8. PDBselect 1992-2009 and PDBfilter-select.

9. Learning sparse models for a dynamic Bayesian network classifier of protein secondary structure.

10. Data growth and its impact on the SCOP database: new developments.

1. Membrane protein structure predictions for exploration.

2. Unexpected features of the dark proteome.

3. Analysis of 51 cyclodipeptide synthases reveals the basis for substrate specificity.

4. Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning.

5. Accurate disulfide-bonding network predictions improve ab initio structure prediction of cysteine-rich proteins.

6. Protein-fold recognition using an improved single-source K diverse shortest paths algorithm.

7. Genomic analysis of 38 Legionella species identifies large and diverse effector repertoires.

8. CRISPRcasIdentifier: Machine learning for accurate identification and classification of CRISPR-Cas systems.

9. The PFP and ESG protein function prediction methods in 2014: effect of database updates and ensemble approaches.

10. Structure and Assembly of the Enterohemorrhagic Escherichia coli Type 4 Pilus.