McBASC protocols

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chevron_left Conventional primer design Multiple nucleotide sequence alignment Sequence annotation visualization Amino acid sequence homology search Gene design Multiplex primer design Assembly scaffolding Protein-coding gene prediction Nucleotide sequence homology search Co-evolving residue prediction Primer design DNA design Restriction site detection chevron_right
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McBASC specifications

Information


Unique identifier OMICS_29039
Name McBASC
Alternative name McLachlan Based Substitution Correlation
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes

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  • person_outline Richard Aldrich <>

Publications for McLachlan Based Substitution Correlation

McBASC in pipeline

2017
PMCID: 5506539
PMID: 28751967
DOI: 10.5256/f1000research.12138.r21733

[…] the 3d structure of a representative protein (pdb code: 1dj0) from the pseudouridine synthase domain family (cdd code: cd01291). 8, 30, 20 and 46 coevolutionary connections were predicted by mip , mcbasc , dca and psicov23 methods, respectively. interestingly, in this family, the average conservation score (al2co score: 0.65) for all sites are quite low (as shown by color coding), despite […]


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McBASC in publications

 (13)
PMCID: 5506539
PMID: 28751967
DOI: 10.5256/f1000research.12138.r21733

[…] coevolved site pairs (located within 10å spatial distance), which were identified by approaches, such as mutual information (mip program ), mclachlan amino acid similarity matrix based techniques (mcbasc program ), direct coupling analysis (dca program ), and protein sparse inverse covariance method (psicov program ), from 753 curated protein family alignments, available from the conserved […]

PMCID: 4939391
PMID: 27441044
DOI: 10.1016/j.csbj.2016.06.002

[…] of multiple sequence alignments (msa) in the absence of structural information, as has been done through algorithms including statistical coupling analysis (sca , , ), mutual information (mi ), mclachlan based substitution correlation (mcbasc ) and observed minus expected square (omes ). a more thorough evaluation of these methods is found in livesay et al. (2012) ., the sca method […]

PMCID: 4901368
PMID: 27074285
DOI: 10.1021/acs.chemrev.5b00631

[…] to mi.− further, methods to estimate baseline values for correlation (e.g., resampling or sequence shuffling) can improve mi analysis.,,, another relatively direct coevolution metric, the mclachlan-based substitution correlation (mcbasc), looks for similar patterns of variation in the columns of an msa, weighting for residue similarity using the mclachlan scoring matrix. analogous […]

PMCID: 4719070
PMID: 25971595
DOI: 10.1093/bib/bbv027

[…] [], scoring of docking decoys [] as well as in protein–protein interface prediction [, ] (e)., early applications of co-evolution to protein interface prediction include omes [], mi [] sca [], mcbasc [], elsc [] and the more recent i-patch [] and evcomplex []. the earlier methods generally suffer from low precision (20–25% precision at 20% recall) []. the more recent method, i-patch, […]

PMCID: 3877293
PMID: 24391951
DOI: 10.1371/journal.pone.0084398

[…] algorithms rank different pairs as the most strongly co-evolving , with no single algorithm clearly more “correct” than others. thus, for this work, we used five common methods – znmi, omes, mcbasc, elsc and sca – that employ divergent strategies to detect evolutionary constraints. znmi uses information theory ; omes calculates a goodness-of-fit-like statistical parameter , ; mcbasc […]


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McBASC institution(s)
Department of Molecular and Cellular Physiology, and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
McBASC funding source(s)
Supported by the Mathers Foundation.

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