MARCOIL protocols

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MARCOIL specifications

Information


Unique identifier OMICS_09324
Name MARCOIL
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Protein sequence
Input format FASTA
Output data HMM based on MTIDK and other matrices
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Mauro Delorenzi <>

Information


Unique identifier OMICS_09324
Name MARCOIL
Interface Web user interface
Restrictions to use None
Input data Protein sequence
Input format FASTA
Output data HMM based on MTIDK and other matrices
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Mauro Delorenzi <>

Publication for MARCOIL

MARCOIL in pipelines

 (2)
2016
PMCID: 5630835
PMID: 27189989
DOI: 10.1093/gbe/evw087

[…] bayesian posterior probabilities (10,000,000 generations)., the ncbi cd-search was used to identify conserved domains. secondary structure elements and folds were predicted in phyre2 (). pcoils and marcoil (http://toolkit.tuebingen.mpg.de) were used for prediction of coiled-coil regions and the presence of heptad repeats., phytophthora p. infestans rna was kindly provided by sebastian […]

2013
PMCID: 3703794
PMID: 23862152
DOI: 10.1155/2013/697051

[…] used to predict the molecular changes associated with amino acid variants []. it uses sift, psi-blast, and pfam profiles along with some structural disorder prediction algorithms, including tmhmm, marcoil, i-mutant 2.0, b-factor prediction, and disprot []. functional analysis includes the prediction of dna-binding site, catalytic domains, calmodulin-binding targets, and posttranslational […]

MARCOIL in publications

 (61)
PMCID: 5801592
PMID: 29456547
DOI: 10.3389/fpls.2018.00071

[…] hsf proteins were defined by merging the results from the pfam (http://pfam.xfam.org/), the heatster (http://www.cibiv.at/services/hsf/), the smart (http://smart.embl-heidelberg.de/), and the marcoil (http://toolkit.tuebingen.mpg.de/marcoil) programs. the aha, nuclear localization signal (nls), nuclear export signal (nes) and rd structures were detected based on the heatster […]

PMCID: 5715377
PMID: 29250042
DOI: 10.3389/fmicb.2017.02287

[…] long. sequence analyses were performed in the mpi bioinformatics toolkit (alva et al., ; https://toolkit.tuebingen.mpg.de) using quick2d, hhpred (hildebrand et al., ), pcoils (lupas et al., ), and marcoil (delorenzi and speed, ). transmembrane segments were predicted with fmhmm (sonnhammer et al., ) and phobius (käll et al., ). for transcriptional fusions, comparisons between samples […]

PMCID: 5658623
PMID: 28840964
DOI: 10.1111/1751-7915.12820

[…] with coiled‐coil interacting regions(maestro et al., ; mezzina and pettinari, ). this common structure suggests that the mode of oligomerization could be determined by the coiled‐coil regions. using marcoil (delorenzi and speed, ; mezzina et al., ), phapaz was found to have a maximum probability of 32% of coiled‐coil regions for homo‐oligomerization, while phaptd contains a high coiled‐coil […]

PMCID: 5558467
PMID: 28840100
DOI: 10.1016/j.gdata.2017.08.004

[…] cc motifs , . we have used these signature sequences to classify the non-tnl family. the presence of cc regions was further validated by hmmer search (phmmer) against uniprotkb protein database and marcoil server using 9fam matrix. the probability of n-terminal region showing coiled coil conformation in the marcoil plot was in the range of 0.4-1 for most of the non-tnl proteins., the canonical […]

PMCID: 5553167
PMID: 28615210
DOI: 10.1128/JVI.00304-17

[…] data strongly suggested that the heptad repeat and, therefore, most likely a coiled-coil motif in this n-terminal portion of the protein likely played a role in inducing the mt effects., using the marcoil coiled-coil prediction algorithm (, ) to analyze the primary rrv orf52 sequence, we noted that the polypeptide encompassing residues 14 to 39 and containing the heptad repeats had a 50 to 97% […]

MARCOIL institution(s)
Genetics and Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia

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