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GeneMark.hmm specifications


Unique identifier OMICS_29662
Name GeneMark.hmm
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for GeneMark.hmm

GeneMark.hmm citations


Comparative Genomics Reveals the Core Gene Toolbox for the Fungus Insect Symbiosis

PMCID: 5954228
PMID: 29764946
DOI: 10.1128/mBio.00636-18

[…] 7b (), corresponding to fungal sequences from RepBase (). The genomes were annotated with the Funannotate v0.6.2 pipeline (, employing tools of Augustus (), GeneMark.hmm-ES (), and EVM (). Gene function was inferred from matches to the databases of Pfam (), Merops (), CAZy (), InterProScan (), and Swiss-Prot (). Product descriptions were assigned with hom […]


Comparative genomics of the wheat fungal pathogen Pyrenophora tritici repentis reveals chromosomal variations and genome plasticity

BMC Genomics
PMCID: 5913888
PMID: 29685100
DOI: 10.1186/s12864-018-4680-3

[…] mbination of supporting protein and transcript alignments and ab initio predictions on a repeat masked genome, with minimum intron length of 10 bp and weights for ab initio prediction CodingQuarry:1, GeneMark.hmm:1, BFP protein exonerate:2.Gene predictions for the M4 and BFP mitochondrial genomes were made using Mitos webserver [] and refined based on blast versus prote […]


Complete Genome Sequence of Agrobacterium tumefaciens 1D1609

Genome Announc
PMCID: 5908930
PMID: 29674541
DOI: 10.1128/genomeA.00253-18

[…] CR and Sanger sequencing. The iterative process was continued until the complete genome assembly was obtained and verified. Gene prediction was done using RNAmmer (), tRNAscan-SE (), Prodigal (), and GeneMark.hmm (). The initial annotation was based on the homologous genes in A. tumefaciens C58 () and Ach5 () as identified by OrthoMCL (). Subsequently, manual curation was performed based on BLASTP […]


Vast diversity of prokaryotic virus genomes encoding double jelly roll major capsid proteins uncovered by genomic and metagenomic sequence analysis

Virol J
PMCID: 5894146
PMID: 29636073
DOI: 10.1186/s12985-018-0974-y

[…] Protein coding sequences in contigs obtained as described above were predicted using GeneMark hmm prokaryotic and translated (version 3.25) []., The resulting proteins sequences were used as queries to search the nr database using PSI-BLAST, the Conserved Domain Database (CDD) using R […]


Molecular cloning, expression, and functional characterization of the β agarase AgaB 4 from Paenibacillus agarexedens

PMCID: 5874223
PMID: 29594843
DOI: 10.1186/s13568-018-0581-8
call_split See protocol

[…] For the de novo assembly of the complete genome, we used Velvet (Zerbino and Birney ) to assemble paired-end and mate-pair reads to scaffolds. Genes on these assembled scaffolds were predicted using GeneMark.hmm (Besemer and Borodovsky ) and were annotated using a BLAST (blastp) search against the NCBI nr protein database, with an e-value cutoff of 0.00001. For the functional annotation of predic […]


Genome Organization of Escherichia Phage YD 2008.s: A New Entry to Siphoviridae Family

PMCID: 5893235
PMID: 29644014
DOI: 10.21315/tlsr2018.29.1.3
call_split See protocol

[…] s genome, formation of DNA, GC contents and nucleotide (A, T, C, G) compositions details were obtained from CLC Genomic Workbench 6.0. Predictions of open reading frames (ORFs) were carried out using GeneMark. hmm v3.25 (; ) and confirmed with RAST server (). Nucleotide and protein sequences were subjected to search against NCBI BLAST (Basic Local Alignment Search Tool) tools to search for homolog […]


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GeneMark.hmm institution(s)
Schools of Biology and Mathematics, Georgia Institute of Technology, Atlanta, GA, USA
GeneMark.hmm funding source(s)
Supported in part by the National Institutes of Health.

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