R/search_phmmer.R
search_phmmer.RdPerform a phmmer search of a protein sequence against a protein sequence database.
search_phmmer(seq, seqdb = "swissprot", timeout = 180, verbose = FALSE)A character vector containing the sequences of the query or any other object that can be converted to that. It can also be a URL or the path to a FASTA file.
A character vector containing the target databases. Frequently
used databases are swissprot, uniprotrefprot, uniprotkb,
ensembl,
pdb and alphafold, but a complete and updated list is available at
https://www.ebi.ac.uk/Tools/hmmer/.
Set maximum request time in seconds.
A logical, if TRUE details of the download process is printed.
An Data Frame containing the results from HMMER.
search_phmmer(
seq = "MTEITAAMVKELRTGAGMMDCKN",
seqdb = "pdb",
verbose = FALSE
)
#> # A tibble: 7 × 47
#> algori…¹ uuid stats…² stats…³ stats…⁴ stats.Z stats…⁵ stats…⁶ stats…⁷ stats…⁸
#> <chr> <chr> <dbl> <int> <chr> <dbl> <int> <int> <int> <int>
#> 1 phmmer 9B24… 1 7 0.06 546676 0 1960 7 546676
#> 2 phmmer 9B24… 1 7 0.06 546676 0 1960 7 546676
#> 3 phmmer 9B24… 1 7 0.06 546676 0 1960 7 546676
#> 4 phmmer 9B24… 1 7 0.06 546676 0 1960 7 546676
#> 5 phmmer 9B24… 1 7 0.06 546676 0 1960 7 546676
#> 6 phmmer 9B24… 1 7 0.06 546676 0 1960 7 546676
#> 7 phmmer 9B24… 1 7 0.06 546676 0 1960 7 546676
#> # … with 37 more variables: stats.user <dbl>, stats.domZ_setby <int>,
#> # stats.n_past_bias <int>, stats.sys <dbl>, stats.n_past_fwd <int>,
#> # stats.total <dbl>, stats.nmodels <int>, stats.nincluded <int>,
#> # stats.n_past_vit <int>, stats.nreported <int>, stats.domZ <dbl>,
#> # hits.archScore <chr>, hits.ph <chr>, hits.arch <chr>, hits.kg <chr>,
#> # hits.ndom <int>, hits.extlink <chr>, hits.taxid <chr>, hits.acc <chr>,
#> # hits.taxlink <chr>, hits.desc <chr>, hits.pvalue <dbl>, hits.seqs <list>, …