create_consensus_topology_conservation: Create a consensus-topology-conservation table

In richelbilderbeek/bbbq: The Bilderbeek Bianchi and Bogaart Question

Create a consensus-topology-conservation table

Description

Create a consensus-topology-conservation table

Usage

create_consensus_topology_conservation(
  protein_sequences,
  topology_prediction_tool,
  msa_method,
  msa_subst_matrix,
  msa_filename = NULL
)

Arguments

protein_sequences	one or more protein sequences
topology_prediction_tool	tool to predict the topology of a membrane protein. Possible values are: mhcnuggetsr pureseqtmr, which uses PureseqTM mhcnuggetsr tmhmm, which uses TMHMM
msa_method	the method argument of msa. Valid methods are ClustalW, ClustalOmega (preferred for proteins) and Muscle
msa_subst_matrix	multiple sequence alignment substitution matrix, the substitutionMatrix argument of msa. For a protein alignment, relevant values are blosum, pam and gonnet
msa_filename	filename to save the multiple sequence alignment to. Use NULL if there is no desire to store it

Value

a tibble with columns:

• aa the amino acid at that position in consensus sequence

• score the conservation score

• is_tmh if that amino acid at that location is part of a transmembrane helix

richelbilderbeek/bbbq documentation built on July 27, 2023, 2:15 a.m.