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phmmer specifications


Unique identifier OMICS_24342
Name phmmer
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained No



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phmmer citations


Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica

PLoS Genet
PMCID: 5940178
PMID: 29738521
DOI: 10.1371/journal.pgen.1007333

[…] . We also tested the accuracy of the full model on a collection of alternative strains related to the training dataset (see ). Orthologs to the top genes identified by our model were identified using phmmer from the HMMER3.0 package ( Additional notes on model building and testing are provided in .We tested the top 196 genes for the presence of independent mutations in each serov […]


Genome wide analysis of the SPL/miR156 module and its interaction with the AP2/miR172 unit in barley

Sci Rep
PMCID: 5935748
PMID: 29728569
DOI: 10.1038/s41598-018-25349-0
call_split See protocol

[…] le ), protein sequences (Table ), and DNA genomic sequences (Table ) of HvSPLs were obtained from the Ensemble H. vulgare database ( database. The pHMMER search function was used, with the A. thaliana SBP domain (Pfam: PF03110) sequence as the query. The IPK Barley BLAST server ( and Phytozome (htt […]


In depth comparative analysis of malaria parasite genomes reveals protein coding genes linked to human disease in Plasmodium falciparum genome

BMC Genomics
PMCID: 5930813
PMID: 29716542
DOI: 10.1186/s12864-018-4654-5

[…] ers are then defined as species group-enriched genes.Fig. 1Each protein sequence of the six Plasmodium species was used as a query and searched against the total protein sequences of these species by phmmer. Figure  shows the numbers of edges and components within the disconnected network using expectation values ranging from 1E − 1 to 1E − 16. Although the relationship between the number of edges […]


Transporter gene acquisition and innovation in the evolution of Microsporidia intracellular parasites

Nat Commun
PMCID: 5923384
PMID: 29703975
DOI: 10.1038/s41467-018-03923-4

[…] a homologues were identified as described in refs. ,,. In brief, Microsporidia protein families were constructed using Markov Clustering with all-against-all sequence similarity scores generated from PHMMER. Putative functions of Microsporidia proteins were inferred using COG annotation of the human or yeast homologue represented in the same cluster. As Microsporidia sequences are often highly div […]


Distribution Patterns of Polyphosphate Metabolism Pathway and Its Relationships With Bacterial Durability and Virulence

Front Microbiol
PMCID: 5932413
PMID: 29755430
DOI: 10.3389/fmicb.2018.00782

[…] The VF sequence package includes 2595 non-redundant core bacterial VFs sourced from VFDB (downloadable from VFDB website; ). The phmmer command from HMMER package was used to search for VF homologs in proteomes using an e-value of 1e-50. Results were all further processed for text mining through a set of short python scripts in […]


Identification of two different chemosensory pathways in representatives of the genus Halomonas

BMC Genomics
PMCID: 5907407
PMID: 29669514
DOI: 10.1186/s12864-018-4655-4

[…] in. The resulting tree converged with all nodes supported with a posterior probability > 0.5.Halomonas sp. genomes (Additional file : Table S1), Swissprot and PDB were scanned with a cheA query using Phmmer [] in an iterative approach. Resulting sequences were aligned with MAFFT 7 [] and manually inspected. Phylogenetic analyses were performed with the maximum likelihood package PhyML3 []. All seq […]

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