NORSNET_ROOT
Overrides /usr/share/norsnet, the path to helper scripts and data files.
norsnet1
Identifies unstructured loops from sequence
Usage
norsnet <FASTA_FILE>
<RDBPROF_FILE>
<HSSP_FILE>
<OUTPUT_FILE>
<PROTEIN_NAME>
<PROFBVAL_FILE>
<OUTPUT_MODE>
<DEBUG>
Overview
NORSnet is a neural network based method that focuses on the identification of unstructured loops.
NORSnet was trained to distinguish between very long contiguous segments with non-regular secondary structure (NORS regions) and well-folded proteins. NORSnet was trained on predicted information rather than on experimental data. Therefore, it was optimized on a large data, which is not biased by today's experimental means of capturing disorder. Thus, NORSnet reached into regions in sequence space that are not covered by the specialized disorder predictors. One disadvantage of this approach is that it is not optimal for the identification of the "average" disordered region.
Conversion of PSI-BLAST alignment to HSSP format
The most up-to-date procedure can be found at <https://www.rostlab.org/owiki/index.php/How_to_generate_an_HSSP_file_from_alignment#Generating_an_HSSP_profile>.
- 1. Convert BLAST output to a Single Alignment Format (SAF):
-
/usr/share/librg-utils-perl/blast2saf.pl fasta=<query_fasta_file> maxAli=3000 eSaf=1 \saf=<saf_formatted_file> <blast_output>
- 2. Convert SAF format to HSSP:
-
/usr/share/librg-utils-perl/copf.pl <saf_formatted_file> formatIn=saf formatOut=hssp \fileOut=<hssp_formatted_file> exeConvertSeq=convert_seq
- 3. Filter results to 80% redundancy:
-
/usr/share/librg-utils-perl/hssp_filter.pl red=80 <hssp_formatted_file> fileOut=<filtered_hssp_formatted_file>
Output format
Output mode 1
Tabular output, columns:
pos amino acid number (1..)res residue 1-letter codenode1 output of neural network node 1node2 output of neural network node 2pred node1 / ( node1 + node2 )n40 pred < 0.40 ? '-' : 'N'n40fil at least 31 AA long stretches of 'N' in n40n59 pred < 0.59 ? '-' : 'N'n59fil at least 31 AA long stretches of 'N' in n59
'N' is for non-regular secondary structure.
References
- Schlessinger, A., Liu, J., and Rost, B. (2007). Natively unstructured loops differ from other loops. PLoS Comput Biol, 3(7), e140.
Options
- FASTA_FILE
-
File containing protein amino-acid sequence in fasta format.
- RDBPROF_FILE
-
Secondary structure and solvent accessibility prediction by PROF in rdb format.
- HSSP_FILE
-
PSI-BLAST alignment profile file converted to HSSP format.
- OUTPUT_FILE
-
The name of the final NORSnet output file.
- PROFBVAL_FILE
-
Flexible/rigid residues prediction by profbval(1) in rdb format (mode 5).
- OUTPUT_MODE
-
NORSnet can create output files in different formats for different purposes. Valid modes are `1', `2' or `3'. Default mode: 1.
- -
-
Default mode. Use this when you do not want to give a value here but you want to specify
debug.
- 1
-
for metadisorder(1)
- DEBUG
-
Set to 1 for debugging messages
Output
number -
|
residue number |
|---|---|
residue -
|
residue type |
raw -
|
raw value of the different between the two output nodes |
Examples
norsnet /usr/share/doc/norsnet/examples/cad23.f /usr/share/doc/norsnet/examples/cad23-fil.rdbProf /usr/share/doc/norsnet/examples/cad23-fil.hssp cad23.norsnet cad23 /usr/share/doc/norsnet/examples/cad23.profbvalEnvironment
Files
-
*.norsnet -
default output file extension
-
/usr/share/doc/norsnet/examples -
default precomputed input files directory
Notes
- 1. It is recommended to create the profiles using 3 iteration of PSI-BLAST against big database
- 2. It is also recommended to filter the hssp files using hssp_filter.pl from the Prof package using the following command: perl hssp_filter.pl hssp_file red=80
Releases
6 releases since Debian 8 (Jessie); the text changed 4 times.