SSNpipe Usage Examples - ahvdk/SSNpipe GitHub Wiki

The examples provided here use a sequence dataset included in the SSNpipe directory/examples/clanB.fasta. The dataset contain 278 biochemically characterized proteins from Glycoside Hydrolase Family 7 (GH7, 74 sequences) and Glycoside Hydrolase Family 16 (GH16, 204 sequences), which shares a common ancestor and constitutes clan B in the Carbohydrate Active Enzymes database.

“Create SSNs”

…from sequences in a FASTA file.

  1. Use clanB.fasta from the SSNpipe examples folder as input.
  2. Pick a results folder.
  3. Fill in a description. This is written to the log file.
  4. Select E-value as parameter.
  5. Set the thresholds to minimum: 0, maximum: 10, and step: 5.
  6. Set output format to Cytoscape.
  7. Click “Generate SSNs”.

This will create: • 1.1 Main results directory • 1.1.1 Log file • 1.1.2 Error file • 1.1.3 MASTER.txt file • 1.1.4 NodeTable_ff.txt file • 1.2 “networks” subfolder • 1.2.1 NETWORK_ff_pp_n_.txt files

 

“Refine SSNs”

…from a MASTER.txt file.

  1. Use the MASTER.txt file in the main results directory chosen in 2.1: “Create SSNs” as input.
  2. SSNPipe will set the results folder to the results folder created in 2.1: “Create SSNs”
  3. Select E-value as parameter.
  4. Set the thresholds to minimum: 15, maximum: 60, and step: 5.
  5. Set output format to Cytoscape.
  6. Click “Refine SSNs”.

This will create: • 1.1.1 Log file • 1.1.2 Error file • 1.2.1 NETWORK_ff_pp_n_.txt files

 

“Create Metanodes”

…for a large network.

  1. Use the NETWORK_cs_ev_0_.txt from the networks subfolder chosen in 2.1: “Create SSNs” as input.
  2. SSNPipe will set the results folder to the results folder created in 2.1: “Create SSNs” as results folder.
  3. Click “Initiate”.
  4. Set Metanodes threshold to 5.
  5. Click “Create Metanodes”.

This will create: • 1.1.1 Log file • 1.1.2 Error file • 1.3 “metanodes” subfolder • 1.3.1 Metanodes_n_m_Info.txt file • 1.3.2 METANODES-NETWORKS_ff_pp_n_m_.txt file

 

“Group Analysis”

…of a network, to know which sequences belong to each group.

  1. Use the NETWORKS_cs_ev_5_.txt in the networks subfolder chosen in 2.1: “Create SSNs” as input file.
  2. SSNPipe will set the results folder to the results folder created in 2.1: “Create SSNs” as results folder.
  3. Click “Initiate”.
  4. Click “Run Analysis”.

This will create: • 1.1.1 Log file • 1.1.2 Error file • 1.4 “analysis” subfolder • 1.4.1 GROUPS_n_Info.txt file

In this example 204 sequences (GH16) belong to group 1, and 74 sequences (GH7) belong to group 2. Sequences not belonging to any group are indicated with a 0, however, in this example there are none.