dfam.query | R Documentation |
Validate or annotate putative LTR
transposons that have been predicted using LTRharvest
, LTRdigest
, or LTRpred
.
dfam.query( seq.file, Dfam.db = NULL, eval = 0.001, cores = 1, output.folder = getwd() )
seq.file |
file path to the putative LTR transposon sequences in |
Dfam.db |
folder path to the local Dfam database or |
eval |
E-value threshhold to perform the HMMer search against the Dfam database. |
cores |
number of cores to use to perform parallel computations. |
output.folder |
folder path to store the annotation results. |
The Dfam database provides a collection of curated transposable element annotations.
Hajk-Georg Drost
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