norsnet - Online in the Cloud

PROGRAM:

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) 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.

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