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M-pick specifications

Information


Unique identifier OMICS_01447
Name M-pick
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for M-pick

M-pick citations

 (3)
library_books

Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods

2015
Ecol Evol
PMCID: 4461425
PMID: 26078860
DOI: 10.1002/ece3.1497

[…] erence sequences known a priori) use a hierarchical or greedy heuristic approach (Sun et al. ), although a few new developments use alternative statistical or modularity-based approaches (e.g., CROP, M-Pick, SWARM, Table). In general, hierarchical algorithms compute sequence divergence between all pairs of sequences – which is very computationally demanding – producing a distance matrix before gen […]

library_books

The intellectual disability protein RAB39B selectively regulates GluA2 trafficking to determine synaptic AMPAR composition

2015
Nat Commun
PMCID: 4383008
PMID: 25784538
DOI: 10.1038/ncomms7504

[…] immunofluorescence at 14 DIV. We found an increase in PICK1, GluA2 and GluA3 levels in the cell body of shRab39b-treated neurons as compared with the neurons treated with the control shRNA (mean±s.e.m., PICK1 shScramble n=21: 2.98±0.28, shRab39b n=21: 4.25±0.35; t-test P=0.009; GluA2 shScramble n=9: 0.60±0.05, shRab39b n=5: 0.88±0.05; t-test P=0.003; GluA3 shScramble n=6: 0.42±0.03, shRab39b n=7: […]

library_books

Ecological Consistency of SSU rRNA Based Operational Taxonomic Units at a Global Scale

2014
PLoS Comput Biol
PMCID: 3998914
PMID: 24763141
DOI: 10.1371/journal.pcbi.1003594

[…] , >80% of all non-singleton OTUs at different clustering thresholds were monophyletic ().In general, conceptually more sophisticated algorithms to demarcate OTUs such as ecotype simulation , CROP or M-Pick may be suited for focused problems, but arguably suffer from throughput problems due to high computational demands (we were not able to execute any of them on our set of one million sequences) […]

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M-pick institution(s)
Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA; Department of Electrical and Computer Engineering, University of Florida, Gainesville, FL, USA; Department of Microbiology and Immunology, Center of Excellence in Bioinformatics & Life Sciences, Department of Computer Science and Engineering, The State University of New York at Buffalo, Buffalo, NY, USA
M-pick funding source(s)
This work is supported in part by National Science Foundation under grant No. DBI-1062362.

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