Difference between revisions of "SCRATCH-1D"

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[[Category:Software]][[Category:biology]][[Category:NGS]]
 
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|{{#vardefine:app|scratch1d}}
 
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|{{#vardefine:url|REPLACE}}
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|{{#vardefine:url|http://download.igb.uci.edu/}}
 
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SCRATCH-1D currently includes the following predictors and tools:
 
SCRATCH-1D currently includes the following predictors and tools:
* SSpro     Release 5.Protein secondary structure prediction (3-class)
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* SSpro8     Release 5.Protein secondary structure prediction (8-class)
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*   SSpro release 6.0 (2021) : Protein secondary structure prediction (3-class)
* ACCpro     Release 5.Protein relative solvent accessibility prediction (at the 25% threshold)
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*   SSpro8 release 6.0 (2021) : Protein secondary structure prediction (8-class)
* ACCpro20   Release 5.Protein relative solvent accessibility prediction (thresholds 0% to 95%)
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*   ACCpro release 6.0 (2021) : Protein relative solvent accessibility prediction (at the 25% threshold)
* PROFILpro Release 1.Protein evolutionary information / sequence profiles for 1D predictors
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*   ACCpro20 release 6.0 (2021) : Protein relative solvent accessibility prediction (thresholds 0% to 95%)
* HOMOLpro   Release 1.Homology-based secondary structure & solvent accessibility prediction
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*   EVALpro release 1.0 (2019) : Evaluation of sequence-based & profile-based predictors
* 1D-BRNN    Release 3.3  One-dimensional bidirectional recurrent neural networks
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*    PROFILpro release 2.0 (2021) : Protein evolutionary information / sequence profiles
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*   HOMOLpro release 2.0 (2021) : Homology-based secondary structure & solvent accessibility prediction
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
 
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==

Latest revision as of 20:35, 12 August 2022

Description

scratch1d website  

SCRATCH-1D is a suite of one-dimensional predictors included in the long-established and widely used SCRATCH suite of predictors developed by the Institute for Genomics and Bioinformatics (IGB) of the University of California, Irvine (UCI).

SCRATCH-1D currently includes the following predictors and tools:

  • SSpro release 6.0 (2021) : Protein secondary structure prediction (3-class)
  • SSpro8 release 6.0 (2021) : Protein secondary structure prediction (8-class)
  • ACCpro release 6.0 (2021) : Protein relative solvent accessibility prediction (at the 25% threshold)
  • ACCpro20 release 6.0 (2021) : Protein relative solvent accessibility prediction (thresholds 0% to 95%)
  • EVALpro release 1.0 (2019) : Evaluation of sequence-based & profile-based predictors
  • PROFILpro release 2.0 (2021) : Protein evolutionary information / sequence profiles
  • HOMOLpro release 2.0 (2021) : Homology-based secondary structure & solvent accessibility prediction


Environment Modules

Run module spider scratch1d to find out what environment modules are available for this application.

System Variables

  • HPC_SCRATCH1D_DIR - installation directory




Citation

If you publish research that uses scratch1d you have to cite it as follows:

  • C.N. Magnan & P. Baldi (2014). SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity.

Bioinformatics, vol 30 (18), 2592-2597

  • J. Cheng, A. Randall, M. Sweredoski, & P. Baldi. SCRATCH: a Protein Structure and Structural Feature Prediction Server.

Nucleic Acids Research, vol. 33 (web server issue), w72-76, (2005)