---
name: "norsnet"
section: "1"
platform: "linux"
package: "norsnet"
version: "1.0.17-7"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/norsnet"
---

# norsnet(1)

identifies unstructured loops from sequence

## NAME

norsnet - identifies unstructured loops from sequence

## SYNOPSIS

norsnet \<FASTA\_FILE\> \<RDBPROF\_FILE\> \<HSSP\_FILE\> \<OUTPUT\_FILE\> \<PROTEIN\_NAME\> \<PROFBVAL\_FILE\> \<OUTPUT\_MODE\> \<DEBUG\>

## DESCRIPTION

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 code
 node1          output of neural network node 1
 node2          output of neural network node 2
 pred           node1 / ( node1 + node2 )
 n40            pred < 0.40 ? '-' : 'N'
 n40fil         at least 31 AA long stretches of 'N' in n40
 n59            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)](/profbval/1.md) 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.profbval
```

## ENVIRONMENT

- NORSNET\_ROOT

  Overrides /usr/share/norsnet, the path to helper scripts and data files.

## 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

  ## AUTHOR

A. Schlessinger \<avnersch@gmail.com\>

## SEE ALSO

- [**profbval**(1)](/profbval/1.md), [**prof**(1)](/prof/1.md).

  - Main website

  \<http://www.predictprotein.org/\>