Supplementary files to methods and results section.

About.

These scripts can be used to mine database files from UniProt and TopDB into transmembrane and perform sequence distribution data analysis.

Disclaimer: This release is not designed for redistribution, or reapplication as production software, but is provided as is. If you are having trouble running the scripts, or if there is something unclear, do feel free to contact the authors directly.

Download.

The downloaded zip includes the original files downloaded from the respective databases and the Uniprot non-redundant datasets. The zip also contains the python scripts used to generate the datasets, tables, figures, as well as the parsed .csv files of each dataset. Within the .csv files is the ID for the respective databases, the full protein sequence, the TMH sequences, the flank sequences (each file for each dataset has a different cut-off flank length: 5, 10 or 20), the number of TMHs in the given protein, and the orientation of the TMH.

• Click here to download the datasets.
• Click here to download the scripts.
• Click here to download the original database files from Uniprot.
• Click here to visit the TopDB site to download the database.

Databases.

UniArch.txt
	
UniBacilli.txt
	
UniCress.txt
	
UniER.txt
	
UniEcoli.txt
	
UniFungi.txt
	
UniGolgi.txt
	
UniHuman.txt
	
UniPM.txt
	

Scripts.

Scripts.zip includes scripts used for many of the figures and tables throughout the results:

Figure_1_2_3_4_6.py
	
Figure_5A_vectors.py
	
Figure_5B_vectors.py
	
Figure_7.py
	
Figure_S1.py
	
Figure_S4.py
	
Table_1.py
	
Table_2_central_alignment.py
	
Table_2_database_defined.py
	
Table_4.py
	
Table_S1.py
	
Table_S2.py
	
topdb_fasta_dataset_generator.py
	
Uniprot_dataset_generator.py
	

The scripts folder also includes various text files to assist the scripts.

Datasets.

Datasets.zip includes the processed database files used in the distribution analysis throughout the results.

Dataset file name key.

For each of the database files, there are several processed dataset files. The name of the dataset file describes the processing used to generate the dataset file. The csv file names include the name of the original database file, the maximum allowed flank length, the Flankclash variable state (if Flankclash is true, then the dataset does not allow overlap between flanking regions of TMHs. If the variable is false then the dataset allows overlap), and an additional condition if only TMH records with flanks of either half or full length are included in the dataset.

For example, UniPM_20_flanklength_flankclashTrue_only_half_flanks.csv is from the UniPM database file (UniPM), uses a maximum flank length of 20 residues (20_flanklength), does not allow flanks to overlap (FlankclashTrue), and only includes records that have at least 10 residues in both flanks (only_half_flanks).

TopDB_5_flanklength_flankclashFalse_only_full_flanks.csv
	
TopDB_5_flanklength_flankclashFalse_only_half_flanks.csv
	
TopDB_5_flanklength_flankclashFalse.csv
	
TopDB_5_flanklength_flankclashTrue_only_full_flanks.csv
	
TopDB_5_flanklength_flankclashTrue_only_half_flanks.csv
	
TopDB_5_flanklength_flankclashTrue.csv
	
TopDB_10_flanklength_flankclashFalse_only_full_flanks.csv
	
TopDB_10_flanklength_flankclashFalse_only_half_flanks.csv
	
TopDB_10_flanklength_flankclashFalse.csv
	
TopDB_10_flanklength_flankclashTrue_only_full_flanks.csv
	
TopDB_10_flanklength_flankclashTrue_only_half_flanks.csv
	
TopDB_10_flanklength_flankclashTrue.csv
	
TopDB_20_flanklength_flankclashFalse_only_full_flanks.csv
	
TopDB_20_flanklength_flankclashFalse_only_half_flanks.csv
	
TopDB_20_flanklength_flankclashFalse.csv
	
TopDB_20_flanklength_flankclashTrue_only_full_flanks.csv
	
TopDB_20_flanklength_flankclashTrue_only_half_flanks.csv
	
TopDB_20_flanklength_flankclashTrue.csv
	
UniArch_5_flanklength_flankclashFalse_only_full_flanks.csv
	
UniArch_5_flanklength_flankclashFalse_only_half_flanks.csv
	
UniArch_5_flanklength_flankclashFalse.csv
	
UniArch_5_flanklength_flankclashTrue_only_full_flanks.csv
	
UniArch_5_flanklength_flankclashTrue_only_half_flanks.csv
	
UniArch_5_flanklength_flankclashTrue.csv
	
UniArch_10_flanklength_flankclashFalse_only_full_flanks.csv
	
UniArch_10_flanklength_flankclashFalse_only_half_flanks.csv
	
UniArch_10_flanklength_flankclashFalse.csv
	
UniArch_10_flanklength_flankclashTrue_only_full_flanks.csv
	
UniArch_10_flanklength_flankclashTrue_only_half_flanks.csv
	
UniArch_10_flanklength_flankclashTrue.csv
	
UniArch_20_flanklength_flankclashFalse_only_full_flanks.csv
	
UniArch_20_flanklength_flankclashFalse_only_half_flanks.csv
	
UniArch_20_flanklength_flankclashFalse.csv
	
UniArch_20_flanklength_flankclashTrue_only_full_flanks.csv
	
UniArch_20_flanklength_flankclashTrue_only_half_flanks.csv
	
UniArch_20_flanklength_flankclashTrue.csv
	
UniBacilli_5_flanklength_flankclashFalse_only_full_flanks.csv
	
UniBacilli_5_flanklength_flankclashFalse_only_half_flanks.csv
	
UniBacilli_5_flanklength_flankclashFalse.csv
	
UniBacilli_5_flanklength_flankclashTrue_only_full_flanks.csv
	
UniBacilli_5_flanklength_flankclashTrue_only_half_flanks.csv
	
UniBacilli_5_flanklength_flankclashTrue.csv
	
UniBacilli_10_flanklength_flankclashFalse_only_full_flanks.csv
	
UniBacilli_10_flanklength_flankclashFalse_only_half_flanks.csv
	
UniBacilli_10_flanklength_flankclashFalse.csv
	
UniBacilli_10_flanklength_flankclashTrue_only_full_flanks.csv
	
UniBacilli_10_flanklength_flankclashTrue_only_half_flanks.csv
	
UniBacilli_10_flanklength_flankclashTrue.csv
	
UniBacilli_20_flanklength_flankclashFalse_only_full_flanks.csv
	
UniBacilli_20_flanklength_flankclashFalse_only_half_flanks.csv
	
UniBacilli_20_flanklength_flankclashFalse.csv
	
UniBacilli_20_flanklength_flankclashTrue_only_full_flanks.csv
	
UniBacilli_20_flanklength_flankclashTrue_only_half_flanks.csv
	
UniBacilli_20_flanklength_flankclashTrue.csv
	
UniCress_5_flanklength_flankclashFalse_only_full_flanks.csv
	
UniCress_5_flanklength_flankclashFalse_only_half_flanks.csv
	
UniCress_5_flanklength_flankclashFalse.csv
	
UniCress_5_flanklength_flankclashTrue_only_full_flanks.csv
	
UniCress_5_flanklength_flankclashTrue_only_half_flanks.csv
	
UniCress_5_flanklength_flankclashTrue.csv
	
UniCress_10_flanklength_flankclashFalse_only_full_flanks.csv
	
UniCress_10_flanklength_flankclashFalse_only_half_flanks.csv
	
UniCress_10_flanklength_flankclashFalse.csv
	
UniCress_10_flanklength_flankclashTrue_only_full_flanks.csv
	
UniCress_10_flanklength_flankclashTrue_only_half_flanks.csv
	
UniCress_10_flanklength_flankclashTrue.csv
	
UniCress_20_flanklength_flankclashFalse_only_full_flanks.csv
	
UniCress_20_flanklength_flankclashFalse_only_half_flanks.csv
	
UniCress_20_flanklength_flankclashFalse.csv
	
UniCress_20_flanklength_flankclashTrue_only_full_flanks.csv
	
UniCress_20_flanklength_flankclashTrue_only_half_flanks.csv
	
UniCress_20_flanklength_flankclashTrue.csv
	
UniEcoli_5_flanklength_flankclashFalse_only_full_flanks.csv
	
UniEcoli_5_flanklength_flankclashFalse_only_half_flanks.csv
	
UniEcoli_5_flanklength_flankclashFalse.csv
	
UniEcoli_5_flanklength_flankclashTrue_only_full_flanks.csv
	
UniEcoli_5_flanklength_flankclashTrue_only_half_flanks.csv
	
UniEcoli_5_flanklength_flankclashTrue.csv
	
UniEcoli_10_flanklength_flankclashFalse_only_full_flanks.csv
	
UniEcoli_10_flanklength_flankclashFalse_only_half_flanks.csv
	
UniEcoli_10_flanklength_flankclashFalse.csv
	
UniEcoli_10_flanklength_flankclashTrue_only_full_flanks.csv
	
UniEcoli_10_flanklength_flankclashTrue_only_half_flanks.csv
	
UniEcoli_10_flanklength_flankclashTrue.csv
	
UniEcoli_20_flanklength_flankclashFalse_only_full_flanks.csv
	
UniEcoli_20_flanklength_flankclashFalse_only_half_flanks.csv
	
UniEcoli_20_flanklength_flankclashFalse.csv
	
UniEcoli_20_flanklength_flankclashTrue_only_full_flanks.csv
	
UniEcoli_20_flanklength_flankclashTrue_only_half_flanks.csv
	
UniEcoli_20_flanklength_flankclashTrue.csv
	
UniER_5_flanklength_flankclashFalse_only_full_flanks.csv
	
UniER_5_flanklength_flankclashFalse_only_half_flanks.csv
	
UniER_5_flanklength_flankclashFalse.csv
	
UniER_5_flanklength_flankclashTrue_only_full_flanks.csv
	
UniER_5_flanklength_flankclashTrue_only_half_flanks.csv
	
UniER_5_flanklength_flankclashTrue.csv
	
UniER_10_flanklength_flankclashFalse_only_full_flanks.csv
	
UniER_10_flanklength_flankclashFalse_only_half_flanks.csv
	
UniER_10_flanklength_flankclashFalse.csv
	
UniER_10_flanklength_flankclashTrue_only_full_flanks.csv
	
UniER_10_flanklength_flankclashTrue_only_half_flanks.csv
	
UniER_10_flanklength_flankclashTrue.csv
	
UniER_20_flanklength_flankclashFalse_only_full_flanks.csv
	
UniER_20_flanklength_flankclashFalse_only_half_flanks.csv
	
UniER_20_flanklength_flankclashFalse.csv
	
UniER_20_flanklength_flankclashTrue_only_full_flanks.csv
	
UniER_20_flanklength_flankclashTrue_only_half_flanks.csv
	
UniER_20_flanklength_flankclashTrue.csv
	
UniFungi_5_flanklength_flankclashFalse_only_full_flanks.csv
	
UniFungi_5_flanklength_flankclashFalse_only_half_flanks.csv
	
UniFungi_5_flanklength_flankclashFalse.csv
	
UniFungi_5_flanklength_flankclashTrue_only_full_flanks.csv
	
UniFungi_5_flanklength_flankclashTrue_only_half_flanks.csv
	
UniFungi_5_flanklength_flankclashTrue.csv
	
UniFungi_10_flanklength_flankclashFalse_only_full_flanks.csv
	
UniFungi_10_flanklength_flankclashFalse_only_half_flanks.csv
	
UniFungi_10_flanklength_flankclashFalse.csv
	
UniFungi_10_flanklength_flankclashTrue_only_full_flanks.csv
	
UniFungi_10_flanklength_flankclashTrue_only_half_flanks.csv
	
UniFungi_10_flanklength_flankclashTrue.csv
	
UniFungi_20_flanklength_flankclashFalse_only_full_flanks.csv
	
UniFungi_20_flanklength_flankclashFalse_only_half_flanks.csv
	
UniFungi_20_flanklength_flankclashFalse.csv
	
UniFungi_20_flanklength_flankclashTrue_only_full_flanks.csv
	
UniFungi_20_flanklength_flankclashTrue_only_half_flanks.csv
	
UniFungi_20_flanklength_flankclashTrue.csv
	
UniGolgi_5_flanklength_flankclashFalse_only_full_flanks.csv
	
UniGolgi_5_flanklength_flankclashFalse_only_half_flanks.csv
	
UniGolgi_5_flanklength_flankclashFalse.csv
	
UniGolgi_5_flanklength_flankclashTrue_only_full_flanks.csv
	
UniGolgi_5_flanklength_flankclashTrue_only_half_flanks.csv
	
UniGolgi_5_flanklength_flankclashTrue.csv
	
UniGolgi_10_flanklength_flankclashFalse_only_full_flanks.csv
	
UniGolgi_10_flanklength_flankclashFalse_only_half_flanks.csv
	
UniGolgi_10_flanklength_flankclashFalse.csv
	
UniGolgi_10_flanklength_flankclashTrue_only_full_flanks.csv
	
UniGolgi_10_flanklength_flankclashTrue_only_half_flanks.csv
	
UniGolgi_10_flanklength_flankclashTrue.csv
	
UniGolgi_20_flanklength_flankclashFalse_only_full_flanks.csv
	
UniGolgi_20_flanklength_flankclashFalse_only_half_flanks.csv
	
UniGolgi_20_flanklength_flankclashFalse.csv
	
UniGolgi_20_flanklength_flankclashTrue_only_full_flanks.csv
	
UniGolgi_20_flanklength_flankclashTrue_only_half_flanks.csv
	
UniGolgi_20_flanklength_flankclashTrue.csv
	
UniHuman_5_flanklength_flankclashFalse_only_full_flanks.csv
	
UniHuman_5_flanklength_flankclashFalse_only_half_flanks.csv
	
UniHuman_5_flanklength_flankclashFalse.csv
	
UniHuman_5_flanklength_flankclashTrue_only_full_flanks.csv
	
UniHuman_5_flanklength_flankclashTrue_only_half_flanks.csv
	
UniHuman_5_flanklength_flankclashTrue.csv
	
UniHuman_10_flanklength_flankclashFalse_only_full_flanks.csv
	
UniHuman_10_flanklength_flankclashFalse_only_half_flanks.csv
	
UniHuman_10_flanklength_flankclashFalse.csv
	
UniHuman_10_flanklength_flankclashTrue_only_full_flanks.csv
	
UniHuman_10_flanklength_flankclashTrue_only_half_flanks.csv
	
UniHuman_10_flanklength_flankclashTrue.csv
	
UniHuman_20_flanklength_flankclashFalse_only_full_flanks.csv
	
UniHuman_20_flanklength_flankclashFalse_only_half_flanks.csv
	
UniHuman_20_flanklength_flankclashFalse.csv
	
UniHuman_20_flanklength_flankclashTrue_only_full_flanks.csv
	
UniHuman_20_flanklength_flankclashTrue_only_half_flanks.csv
	
UniHuman_20_flanklength_flankclashTrue.csv
	
UniPM_5_flanklength_flankclashFalse_only_full_flanks.csv
	
UniPM_5_flanklength_flankclashFalse_only_half_flanks.csv
	
UniPM_5_flanklength_flankclashFalse.csv
	
UniPM_5_flanklength_flankclashTrue_only_full_flanks.csv
	
UniPM_5_flanklength_flankclashTrue_only_half_flanks.csv
	
UniPM_5_flanklength_flankclashTrue.csv
	
UniPM_10_flanklength_flankclashFalse_only_full_flanks.csv
	
UniPM_10_flanklength_flankclashFalse_only_half_flanks.csv
	
UniPM_10_flanklength_flankclashFalse.csv
	
UniPM_10_flanklength_flankclashTrue_only_full_flanks.csv
	
UniPM_10_flanklength_flankclashTrue_only_half_flanks.csv
	
UniPM_10_flanklength_flankclashTrue.csv
	
UniPM_20_flanklength_flankclashFalse_only_full_flanks.csv
	
UniPM_20_flanklength_flankclashFalse_only_half_flanks.csv
	
UniPM_20_flanklength_flankclashFalse.csv
	
UniPM_20_flanklength_flankclashTrue_only_full_flanks.csv
	
UniPM_20_flanklength_flankclashTrue_only_half_flanks.csv
	
UniPM_20_flanklength_flankclashTrue.csv
	

Usage.

Features.

The scripts can be used to mine UniProt files and the Fasta TopDB file into tables that have easier to handle information about their transmembrane domain and neighbouring residue sequences in csv format.

Additional scripts that were used to analyse the data are included, however, these are provided as and may not work out of the box since they rely on more modules.

Generating datasets.

1. These scripts require Biopython, numpy, and python 2.7. Run sudo easy_install pip; sudo pip install numpy; sudo pip install Biopython and enter your password as appropriate. If you come across any errors it is probably because python is not installed in the default locations, or a package has already been installed before you ran these commands.

2. Run the database generator scripts using python topdb_fasta_dataset_generator.py and python Uniprot_dataset_generator.py. These generate csv files from the database files.