Opsins in the Registry

Aim: Make a multiple sequence alignment of opsins sequences present in the registry.

We work on the registry database dump 2022, as described in Querying iGEM Registry SQL Dump Intro.

select part_name 
from parts, parts_seq_features
where parts.part_id = parts_seq_features.part_id
and parts

Retrieve parts from the channel rhodopsin 2.

select part_name, nickname from parts where nickname like "%chr%"

Results Table

part_name	nickname
BBa_S03425	ChR2
BBa_K1634007	pmyo2-ChR2
BBa_K3900056	Chris Prat

What are the parts_seq_features label containing “opsin”?

select label from parts_seq_features  where label like "%opsin%" group by label order by label asc;

Results Table

label
Bacteriorhodopsin
bovine rhodopsin signalling peptide
Green Light Absorbing Proteorhodopsin
Halorhodopsin
mitochondrial proteorhodopsin
Proteorhodopsin
proteorhodopsin 31A08
Sensory Rhodopsin II

Small Tree of Opsins from the Registry

1. Get the opsins in a FASTA file:

select part_name, label, substring(parts.sequence, 
        parts_seq_features.start_pos, 
        parts_seq_features.end_pos
    ) as feature_sequence
from parts
inner join parts_seq_features 
on parts.part_id = parts_seq_features.part_id
where label like "%opsin%" 
into outfile "sql_opsin_features_parts.csv";

26 rows affected.

Converted to .FASTA in ./tmp/sql/sql_opsin_features_parts.fasta.