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Protocols

ConoPrec specifications

Information


Unique identifier OMICS_26899
Name ConoPrec
Interface Web user interface
Restrictions to use None
Input data A or some protein or a nucleic sequence(s).
Input format FASTA,RAW
Output format XLS,TXT,CSV
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline David Craik
  • person_outline Quentin Kaas

Additional information


http://www.conoserver.org/index.php?page=help#conoprec

Publication for ConoPrec

ConoPrec citations

 (7)
library_books

Dietary breadth is positively correlated with venom complexity in cone snails

2016
BMC Genomics
PMCID: 4880860
PMID: 27229931
DOI: 10.1186/s12864-016-2755-6

[…] for the existence of these fragments directly from read depth for sequences that had > 30X coverage. We manually examined sequences flagged by this filter and removed sequences if necessary. We used ConoPrec to remove sequences that did not have a clearly defined signal sequence. Finally, we manually inspected all venom genes to identify any unusual conotoxin transcripts. […]

library_books

High throughput identification of novel conotoxins from the Chinese tubular cone snail (Conus betulinus) by multi transcriptome sequencing

2016
GigaScience
PMCID: 4832519
PMID: 27087938
DOI: 10.1186/s13742-016-0122-9

[…] nt classes according to their published superfamily and family classifications. Second, sequences of each class were aligned with the ClustalW tool [] and the ambiguous results were checked using the ConoPrec tool [] and manual inspection. Finally, a profile HMM was built for the conserved-domain of each class using hmmbuild from the HMMER 3.0 package [] to find the best HMM parameter, and the hmm […]

library_books

Bioinformatics Aided Venomics

2015
Toxins
PMCID: 4488696
PMID: 26110505
DOI: 10.3390/toxins7062159

[…] “EtoR” cleavages, which do not exist in mammals []. Some cleavages seem to be specific of some species, for example the “LtoR” cleavages for which a cone snail proprotein convertase was isolated []. ConoPrec achieved ~80% balanced accuracy for the identification of the 291 verified cone snail toxin cleavage sites in ConoServer, and it was also recently benchmarked to have similar balanced accurac […]

library_books

Molecular Diversity and Gene Evolution of the Venom Arsenal of Terebridae Predatory Marine Snails

2015
Genome Biol Evol
PMCID: 4494067
PMID: 26025559
DOI: 10.1093/gbe/evv104

[…] ogram, termed Pepticomb, was developed and used to analyze the Tr. anilis and Te. subulata transcriptome assemblies. Pepticomb is largely based on source code kindly provided by the developers of the conoprec tool found on the Conoserver website (www.conoserver.org; , ). In stepwise fashion, Pepticomb examines a set of contigs for the presence of a signal sequence, looks for a proregion that termi […]

library_books

Comparison of the Venom Peptides and Their Expression in Closely Related Conus Species: Insights into Adaptive Post speciation Evolution of Conus Exogenomes

2015
Genome Biol Evol
PMCID: 4494072
PMID: 26047846
DOI: 10.1093/gbe/evv109

[…] the sequences with significant hits (e value < 10−5) were translated according to the identified reading frame and were manually inspected. The mature regions of the conopeptides were predicted using ConoPrec (), the redundant and truncated transcripts were excluded from the data set, and the good quality putative conopeptide precursors were collected into the “tribblei conopeptide data set” and “ […]

call_split

Molecular Evolution and Diversity of Conus Peptide Toxins, as Revealed by Gene Structure and Intron Sequence Analyses

2013
PLoS One
PMCID: 3862624
PMID: 24349297
DOI: 10.1371/journal.pone.0082495
call_split See protocol

[…] Gene superfamilies, signal peptides, and cleavage sites of conotoxins were predicted using the ConoPrec tool in ConoServer (http://www.conoserver.org) and the SignalP algorithm (http://www.cbs.dtu.dk/services/SignalP). Identity and similarity assessments were performed using the Basic Local Ali […]

Citations

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ConoPrec institution(s)
Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
ConoPrec funding source(s)
Supported by Australian National Health and Medical Research Council NHMRC (Grant no. 631457) and the Australian Research Council (DP1093115).

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