palmdb: palmdb

In ababaian/palmid: Viral RNA Dependent RNA Polymerase Analysis Suite

palmdb

Description

Palmprint database - initial version (210302) containing GenBank v241 RNA dependent RNA polymerase palmprints

Usage

data(palmdb)

Format

data.frame with 15016 obs of 18 variables

Details

#'

• score. palmscan PSSM motif score. 20+ is high confidence RdRP

• query. input fasta query name

• gene. One of "RdRP" or "RT"

• order. Order of catalytic motifs on input. "ABC" or "CAB"

• confidence. "high" or "low" confidence classification

• qlen. input query length. Is truncated on long input sequences

• pp_start. Start coordinate of palmprint within input sequence

• pp_end. End coordinate of palmprint within input sequence

• pp_length. Length of palmprint sequence (in AA)

• v1_length. Length of v1 region of palmprint

• v2_length. Length of v2 region of palmprint

• pssm_total_score. Raw total score of A,B,C motifs

• pssm_min_score. Lowest scoring PSSM score in palmprint

• motifs. Isolated A,B,C motifs from palmprint.

• super. Isolated super-motif residues from A,B,C (catalytic sites)

• group. Guess of sequence phylum.

• comments. Summary statement on palmprint QC.

Source

palmDB repo

ababaian/palmid documentation built on July 1, 2023, 1:09 a.m.