Man pages for computational-genomics-lab/motifFUN
Searching user-defined motif along with functional annotation filtering criteria
| check_file_existance | For checking file existance |
| check_signalp_version | For checking signalp version |
| check_signalp_version_match | For check signalp program and version match |
| external_programe_existance | For checking programe existance and set default path |
| fasta_to_stockholm | Converts FASTA to STOCKHOLM |
| get_mafft | MAFFT Alignment |
| get_orf | Find and extract open reading frames (ORFs) from nucleotide... |
| get_signalp | Predicts the secretory proteins |
| get_targetp | Predicts sub cellular location of eukaryotic proteins |
| get_tmhmm | Prediction of transmembrane helices in proteins |
| hmmbuild | HMM build |
| hmm_build | HMM build |
| HMM_fasta | Generating HMM resulted fasta file |
| hmm.plot | Plots the relative frequencies of each position for hmmsearch... |
| hmmpress | Prepare a profile database for hmmscan |
| hmm_press | Prepare a profile database for hmmscan |
| hmmsearch | search profile(s) against a sequence database |
| hmm_search | search profile(s) against a sequence database |
| hmm.search | Searching for motifs using HMM searches |
| modify_filename | modifying filenames and set default names |
| orf_discard | Descard ORF file |
| parse_file | Parses single fasta file into multiple files |
| pattern.search | Searching for motifs using regular expressions |
| prepare_inputdata | input data preparation |
| prepare_inputdata_signalp | Preparation of input data to signalp |
| reading_hmm.results | Reading HMM resulted file |
| run_mafft | Running MAFFT Alignment |
| run_signalp | Running signalp |
| run_targetp | FOR running targetp |
| run_tmhmm | FOR running tmhmm |
| siganlp5_summary | Dataframe for signalp |
| summary_motifs | Returns non-redundant sequences from hmm.search or... |
| summary_signalp3 | Dataframe for signalp |
| targetp_summary | Dataframe targetp |
| tmhmm_summary | Dataframe tmhmm |
