search_hmmscan: Perform a hmmscan search of a protein sequence against a...
In currocam/utilsHMMER: HMMERutils
View source: R/search_hmmscan.R
search_hmmscan R Documentation
Perform a hmmscan search of a protein sequence
against a profile-HMM database.
Description
Perform a hmmscan search of a protein sequence
against a profile-HMM database.
Usage
search_hmmscan(seq, hmmdb = "pfam", timeout = 180, verbose = FALSE)
Arguments
seq
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.
hmmdb
A character vector containing the target databases. Frequently
used databases are pfam, tigrfam gene3d, superfamily,
pirsf and treefam, but a complete and updated list is available at
https://www.ebi.ac.uk/Tools/hmmer/.
timeout
Set maximum request time in seconds.
verbose
A logical, if TRUE details of the download process is printed.
Value
An Data Frame containing the results from HMMER.
Examples
search_hmmscan(
seq = "SWYHGPVSRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYHYRINTASDGKLYVSS",
hmmdb = "pfam",
verbose = FALSE
)
currocam/utilsHMMER documentation built on Feb. 19, 2023, 9:54 p.m.
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View source: R/search_hmmscan.R
| search_hmmscan | R Documentation |
Perform a hmmscan search of a protein sequence against a profile-HMM database.
Description
Perform a hmmscan search of a protein sequence against a profile-HMM database.
Usage
search_hmmscan(seq, hmmdb = "pfam", timeout = 180, verbose = FALSE)
Arguments
seq |
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. |
hmmdb |
A character vector containing the target databases. Frequently
used databases are |
timeout |
Set maximum request time in seconds. |
verbose |
A logical, if TRUE details of the download process is printed. |
Value
An Data Frame containing the results from HMMER.
Examples
search_hmmscan(
seq = "SWYHGPVSRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYHYRINTASDGKLYVSS",
hmmdb = "pfam",
verbose = FALSE
)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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