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COACH specifications


Unique identifier OMICS_10034
Alternative name Comparison of Alignments by Constructing Hidden Markov Models
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Robert Edgar

Publication for Comparison of Alignments by Constructing Hidden Markov Models

COACH citations


AlignHUSH: Alignment of HMMs using structure and hydrophobicity information

BMC Bioinformatics
PMCID: 3228556
PMID: 21729312
DOI: 10.1186/1471-2105-12-275

[…] e type and also the scoring scheme used for the alignment of columns in the two profiles. For instance, in the MSA derived profile/PSSM based profile-profile alignment methods, COMPASS [], SALIGN [], COACH [], and others [] have been shown to give better sensitivity (~ 30 - 35%) [] than simple sequence profile search methods such as PSI-BLAST and HMMER2.0 (sensitivity around 20% at superfamily lev […]


Highly Sensitive Detection of Individual HEAT and ARM Repeats with HHpred and COACH

PLoS One
PMCID: 2744927
PMID: 19777061
DOI: 10.1371/journal.pone.0007148

[…] s, the minimum probability cut-off was set to 1%, and the maximum number of hits extended to 500. HHpred returns both E-values and probabilities but we found only E-values useful for this application.COACH can be downloaded as part of the Lobster suite of programs from (as Windows and Linux binaries, and also as source code; a tutorial is available from the same site) […]


Hidden Markov Models and their Applications in Biological Sequence Analysis

Curr Genomics
PMCID: 2766791
PMID: 20190955
DOI: 10.2174/138920209789177575

[…] uence against a multiple alignment or a profile. Comparing sequence profiles can be beneficial for detecting remote homologues, and profile-HMMs have also been used for this purpose [-]. For example, COACH [] allows us to compare sequence alignments, by building a profile-HMM from one alignment and aligning the other alignment to the constructed profile-HMM. HHsearch [] generalizes the traditional […]


Application of nonnegative matrix factorization to improve profile profile alignment features for fold recognition and remote homolog detection

BMC Bioinformatics
PMCID: 2459191
PMID: 18590572
DOI: 10.1186/1471-2105-9-298

[…] ], FUGUE [], and PROSPECT [,] represent the second approach. Currently most remote homolog detection methods are based on profile-profile alignment (PPA). Some examples are SP3 method [], ProfNet [], COACH [], and HMM-HMM comparison method (HHsearch) []. Although these methods are reliable for recognizing relatively close homologs related at the family level, there is still difficulty in finding r […]


A multi template combination algorithm for protein comparative modeling

BMC Struct Biol
PMCID: 2311309
PMID: 18366648
DOI: 10.1186/1472-6807-8-18

[…] LAST, a profile-sequence local alignment method, generates better alignments for the comparative modeling (or easy) targets than the profile-profile alignment methods (e.g., ClustalW [], T-Coffee [], COACH [], and Palign []) we tested, which is consistent with the previous observations (Dr. Kimmen Sjölander, personal communication). However, profile-profile alignment methods are shown to produce b […]


HMM ModE – Improved classification using profile hidden Markov models by optimising the discrimination threshold and modifying emission probabilities with negative training sequences

BMC Bioinformatics
PMCID: 1852395
PMID: 17389042
DOI: 10.1186/1471-2105-8-104

[…] ese proteins, while within each class contain function-specific signals, share fold-specific signals across the functional groups. The development of profile-profile based methods, (e.g. HHSEARCH [], COACH []) maximises the contribution of common signals between profiles, providing even greater sensitivity in detecting remote homologs, and have proven useful for fold classification. Profile HMM da […]


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COACH institution(s)
1195 Roque Moraes Drive, Mill Valley, CA, USA; Department of Bioengineering, University of California, Berkeley, CA, USA

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