NORSNET(1)

📦
version 1.0.17 · 2 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

✨ NORSNET ✨

ok bestie sit DOWN because we're talking about norsnet, a User Command, and it's literally the girl who finds unstructured loops in your sequence 💅

🌸 NAME 🌸

norsnet — identifies unstructured loops from sequence. that's it. that's the job. iconic behavior honestly 🦋

✨ SYNOPSIS ✨

norsnet <FASTA_FILE> <RDBPROF_FILE> <HSSP_FILE> <OUTPUT_FILE>
<PROTEIN_NAME> <PROFBVAL_FILE> <OUTPUT_MODE> <DEBUG>

eight arguments. yes eight. she's high maintenance but she DELIVERS 💖

🧚 DESCRIPTION 🧚

NORSnet is a neural network based method that focuses on the identification of unstructured loops. main character energy fr fr.

so here's the tea: NORSnet was trained to distinguish between very long contiguous segments with non-regular secondary structure (NORS regions) and well-folded proteins. and the way it did that?? it was trained on predicted information rather than on experimental data. no cap. so it was optimized on a large data set that is not biased by today's experimental means of capturing disorder. which means NORSnet reached into regions in sequence space that are not covered by the specialized disorder predictors. ate. 👑

but bestie, there's a tradeoff and we're being honest about it: one disadvantage of this approach is that it is not optimal for the identification of the "average" disordered region. it's giving specialist, not generalist. periodt.

💜 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. go look, i'll wait 🫶

  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>
  1. 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
  1. 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, and the columns are:

  • 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

and just so we're clear: 'N' is for non-regular secondary structure. that's the whole vibe of the letter N here, don't get confused 💖

📚 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
okay yes the OUTPUT_MODE list is a little chaotic in the original and we are preserving that chaos exactly as it was handed to us, no editing the girl's diary 🙈

🌈 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), prof(1).

Main website

ok that's the whole page bestie, you're so ready 🫶 this was version 1.0.17, dated 2022-01-18 — go forth and find those unstructured loops, i'm obsessed with you 💜✨

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