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Protocols

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

Versioning


No version available

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 citations

 (61)
library_books

Evolutionary Origin, Gradual Accumulation and Functional Divergence of Heat Shock Factor Gene Family with Plant Evolution

2018
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 […]

library_books

Characterization of the CrbS/R Two Component System in Pseudomonas fluorescens Reveals a New Set of Genes under Its Control and a DNA Motif Required for CrbR Mediated Transcriptional Activation

2017
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 […]

library_books

Modelling of microbial polyhydroxyalkanoate surface binding protein PhaP for rational mutagenesis

2017
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 […]

library_books

Genome wide identification and tissue specific expression analysis of nucleotide binding site leucine rich repeat gene family in Cicer arietinum (kabuli chickpea)

2017
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 […]

library_books

A Conserved Leucine Zipper Motif in Gammaherpesvirus ORF52 Is Critical for Distinct Microtubule Rearrangements

2017
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% […]

library_books

Predicting the functional consequences of non synonymous single nucleotide polymorphisms in IL8 gene

2017
PMCID: 5529537
PMID: 28747718
DOI: 10.1038/s41598-017-06575-4

[…] related to protein structure, function, and evolution. it uses three servers, sift, psi-blast, and pfam profiles, , along with some structural disorder prediction algorithms, including tmhmm, marcoil, and disprot. thus by combining the scores of all three servers, the accuracy of prediction rises to a greater extent., the nssnp analyzer (http://snpanalyzer.uthsc.edu) is a web based tool […]


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

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