phmmer protocols

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phmmer specifications

Information


Unique identifier OMICS_24342
Name phmmer
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Sean Eddy <>

phmmer in pipelines

 (4)
2018
PMCID: 5798934
PMID: 29345620
DOI: 10.7554/eLife.31662.031

[…] statistics are given in ., the protein sequences of closely-related homologs of e. coli fima, fimc, and fimh were obtained by individual searches the ensembl bacteria genome database () using the phmmer web-server () with a blosum62 (fima) or a blosum90 (fimc and fimh) scoring matrix using the full-length e. coli uti89 protein sequences as queries. the sequence matches were then filtered […]

2017
PMCID: 5290159
PMID: 28128207
DOI: 10.1038/ncomms14246

[…] eukaryotic sequences at reliable values. on the other hand, the n-terminal region was found mainly in bacterial and archaeal nucs, but also in two archaeal proteins annotated as topoisomerases. a phmmer search of the regions of these sequences yielded the n-terminal of nucs., we conducted maximum likelihood (ml) phylogenetic analyses using raxml to construct phylogenetic trees that could […]

2017
PMCID: 5407278
PMID: 28462059
DOI: 10.7717/peerj.3269

[…] which were annotated by mapping to antibiotic resistance genes, virulence factors, bacterial transposases, and prophages obtained respectively from card, patric, interpro, and phast databases using phmmer, with an e-value of at least 1e−10 as the cutoff (; ; ; ; ). rna reads from each sample were filtered by quality (≥q20) and length (≥50 bp) using trimmomatic v0.32 and normalized using seqtk […]

2017
PMCID: 5407278
PMID: 28462059
DOI: 10.7717/peerj.3269

[…] into contigs using idba-ud (). all contigs were searched against the ncbi nt database using blastn and analyzed in megan (). all arcobacter gene sequences were downloaded from ncbi, and using phmmer, arcobacter contigs present in our data were identified with at least 1e−10 e-value as the cutoff. these contigs were extracted and run through the differential coverage binning procedure […]


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phmmer in publications

 (84)
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 (http://hmmer.org). additional notes on model building and testing are provided in ., we tested the top 196 genes for the presence of independent mutations […]

PMCID: 5935748
PMID: 29728569
DOI: 10.1038/s41598-018-25349-0

[…] le ), protein sequences (table ), and dna genomic sequences (table ) of hvspls were obtained from the ensemble h. vulgare database (http://plants.ensembl.org/hordeum_vulgare/info/index) database. the phmmer search function was used, with the a. thaliana sbp domain (pfam: pf03110) sequence as the query. the ipk barley blast server (http://webblast.ipk-gatersleben.de/barley_ibsc/) and phytozome (htt […]

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

[…] are then defined as species group-enriched genes.fig. 1, each 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 […]

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

[…] 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 […]

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

[…] no polyp metabolism enzymes were detected in the group of bacteria., 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 […]


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