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MCAST specifications

Information


Unique identifier OMICS_08378
Name MCAST
Alternative name Motif Cluster Alignment and Search Tool
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data DNA/RNA motifs, DNA sequences
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Version 4.11.0
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline FIMO Team

Information


Unique identifier OMICS_08378
Name MCAST
Alternative name Motif Cluster Alignment and Search Tool
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data DNA/RNA motifs, DNA sequences
Programming languages C
Computer skills Basic
Version 4.11.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline FIMO Team

Publications for Motif Cluster Alignment and Search Tool

MCAST citations

 (18)
library_books

Attachment to Mother and Father at Transition to Middle Childhood

2016
PMCID: 5306151
PMID: 28239249
DOI: 10.1007/s10826-016-0602-7

[…] tantly, partial convergence of attachment representations using the two narrative-based methods could be shown; categorical analysis indicated concordance between attachment to father assessed by the MCAST and secure base scripts assessed by the SBST, and continuous score analysis indicated association between secure base scripts with respect to father as assessed by the MCAST and secure base scri […]

library_books

The Attachment Doll Play Assessment: Predictive Validity with Concurrent Mother Child Interaction and Maternal Caregiving Representations

2016
Front Psychol
PMCID: 5068140
PMID: 27803683
DOI: 10.3389/fpsyg.2016.01594

[…] hat is the most prominent rubric to evaluate attachment patterns in the field provides confidence in the ADPA classification that is not available for other methods, such as the ASCT for example. The MCAST does not differentiate among insecure classification patterns. Most other methods assess doll play in terms of security score (secure vs. insecure), and do not provide classification information […]

library_books

A Simple Predictive Enhancer Syntax for Hindbrain Patterning Is Conserved in Vertebrate Genomes

2015
PLoS One
PMCID: 4489388
PMID: 26131856
DOI: 10.1371/journal.pone.0130413

[…] We submitted the PBX-HOX and MEIS/PREP PWMs derived from the hb+ set to FIMO [] and MCAST [] and used these to search the hb+ and hb- sets. Motifs were considered to co-occur if they occurred within 100bp in the same sequence. […]

library_books

cisMEP: an integrated repository of genomic epigenetic profiles and cis regulatory modules in Drosophila

2014
BMC Syst Biol
PMCID: 4290730
PMID: 25521507
DOI: 10.1186/1752-0509-8-S4-S8

[…] tematic genome-wide CRM screening, we selected five CRM prediction tools which have been verified for Drosophila and are still publicly available []: cisModule [], cisPlusFinder [], ClusterBuster [], MCAST [] and MultiModule []. These methods were based on TFBS clustering or comparative phylogeny. For MCAST and ClusterBuster, statistic models constructed from the features of TFBS clustering are us […]

library_books

Biochemical and bioinformatic methods for elucidating the role of RNA–protein interactions in posttranscriptional regulation

2014
Brief Funct Genomics
PMCID: 4471435
PMID: 24951655
DOI: 10.1093/bfgp/elu020

[…] The read sequences of a PAR-CLIP experiment can be assigned to a positive and negative set using the cluster quality criteria discussed earlier. The HMM used in mCarts is more generic than the one in mcast. It contains only states that represent a motif or a background signal. Transitions between these states are given by a probability combining the distance to the previous motif, the accessibilit […]

library_books

Computational Identification of Active Enhancers in Model Organisms

2013
PMCID: 4357786
PMID: 23685394
DOI: 10.1016/j.gpb.2013.04.002

[…] of the appearance of potential combinatorial TF binding sites . All the TF binding sites are represented by PWM scores and MSCAN returns the significance of the CRM. A similar strategy is adopted in MCAST .To further improve the performance, additional phylogenetic footprinting is employed to align interested orthologous DNA sequences to define a conserved region and then the significance of the […]

Citations

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MCAST institution(s)
Department of Genome Sciences, University of Washington, Seattle, WA, USA; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia; Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA

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