find_seqid {BALCONY}R Documentation

Find sequence identifier by other sequence identifier in given alignment within a specified library

Description

This function allows to find sequence id from alignment file corresponding to the given sequence id. Function requires library of equivalent sequences id defined by user and it is useful to find sequences from other databases in alignment for examined sequence from other database (like PDB sequence for structure and UniProt sequences in alignment).

Usage

find_seqid(sequence_id, library)

Arguments

sequence_id

A string. An ID of e.g. PDB structure identifier

library

A list of vectors which contain a defined by user library e.g. of UniProt ids <-> PDB ids. See examples

Value

seqid

A string. The equivalent ID to the one provided as the input.

Author(s)

Alicja Pluciennik & Michal Stolarczyk

Examples

#creating library uniprot - PDB
lib=list(  c("Q84HB8","4I19","4QA9"),
  c("P34913","4JNC"),
  c("P34914","1EK2","1CR6","1EK1","1CQZ"))
PDB_name = "1CQZ"
find_seqid(PDB_name,lib)

[Package BALCONY version 0.2.10 Index]