Kinannote protocols

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Kinannote specifications

Information


Unique identifier OMICS_05965
Name Kinannote
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
License BSD 2-clause “Simplified” License
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Kinannote

Kinannote in pipelines

 (2)
2016
PMCID: 5037721
PMID: 27598122
DOI: 10.3390/ijms17091442

[…] the predicted proteomes with the family-specific hmm profiles of cazymes downloaded from the dbcan database (available online: http://csbl.bmb.uga.edu/dbcan/download/). kinomes were identified using kinannote []. the neuropeptide-like protein (nlp) and fmrf amide-like peptide (flp) were identified using blastp searches with the known sequences as queries from meloidogyne enterolobii, meloidogyne […]

2015
PMCID: 4491171
PMID: 26108605
DOI: 10.1038/ncomms8344

[…] cutoff ≤10−5) to proteins in at least one of six additional databases: (i) kegg, (ii) flybase (d. melanogaster and related species), (iii) vectorbase (m. domestica), (iv) kinbase using the programme kinannote (http://sourceforge.net/projects/kinannote/), (v) uniprotkb/swiss-prot and (vi) uniprotkb/trembl (november 2014). the final, annotated protein-coding gene set for l. cuprina is accessible […]


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Kinannote in publications

 (7)
PMCID: 5852033
PMID: 29540755
DOI: 10.1038/s41598-018-22816-6

[…] transition. as one of the largest categories enriched in dimorphic ajellomycetaceae but not in saprophytic species was protein kinase activity (table ), we further classified protein kinases using kinannote, including the divergent fungal-specific protein kinase (funk1; methods). we found an expansion of the funk1 family in dimorphic ajellomycetaceae as previously reported,. as we increased […]

PMCID: 5037721
PMID: 27598122
DOI: 10.3390/ijms17091442

[…] glycosyltransferase and polysaccharide lyase, m. enterolobii had gene numbers to code for putative cazymes as 2, 9, 3, 19, 31 and 1, respectively ()., we identified kinases from six nematodes using kinannote and compared the differences between these nematodes. the results showed that m. enterolobii had protein kinases in all twelve types of kinases. compared with other nematodes, m. […]

PMCID: 5015942
PMID: 27412987
DOI: 10.1534/g3.116.032961

[…] the program emboss needle v.6.4.0.0 (), retaining the sequence with the best alignment (spanning ≥ 80% of the query sequence)., fourth, we classified all curated sequences using the program kinannote (), excluding partial sequences of < 200 amino acids in length. sequences not classified using kinannote were assessed for homology to those represented in well-curated kinomes of c. […]

PMCID: 4672506
PMID: 26644012
DOI: 10.1186/s13071-015-1231-5

[…] the kinase sequences, inferred based on the transcriptome, to identify additional kinases not represented as full-length transcripts in the transcriptomic assembly. we employed the program kinannote [] to classify identified protein kinase sequences. if kinases could not be classified using this approach, we used psi-blast v.2.2.26+ [], employing an e-value cut-off of 10−5, to match h. […]

PMCID: 4669435
PMID: 26635209
DOI: 10.1038/srep17759

[…] or position-specific scoring matrices (pssms). however, the combination of several of these methods can achieve enhanced predictions and classification compared with a single method. the program kinannote uses such a combined approach, thereby increasing sensitivity and precision for kinase identification, and was thus employed by us to produce a draft kinome in the first step […]


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Kinannote institution(s)
Broad Institute, 7 Cambridge Center, Cambridge, MA, USA; Massachusetts Institute of Technology, Cambridge, MA, USA

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