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===[[CrocoBLAST:Terminology | Terminology:]]===
===[[CrocoBLAST:Terminology | Terminology:]]===


## [[CrocoBLAST:Terminology#Database | Database]]
# [[CrocoBLAST:Terminology#Database | Database]]
## [[CrocoBLAST:Terminology#Job | Job]]
# [[CrocoBLAST:Terminology#Job | Job]]
## [[CrocoBLAST:Terminology#Queue | Queue]]
# [[CrocoBLAST:Terminology#Queue | Queue]]


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===[[ChargeCalculator:Job_submission | Job submission]]===  
===[[CrocoBLAST:Job_management | Job management]]===  
# [[ChargeCalculator:Job_submission#Upload_molecules | Upload molecules ]]
# [[CrocoBLAST:Job_management#JobSetup | Job setup ]]
# [[ChargeCalculator:Job_submission#Setup_computation | Setup computation ]]
## [[CrocoBLAST:Job_management#JobSetup#CrocoBLASToptions | CrocoBLAST options]]
## [[ChargeCalculator:Job_submission#Set_total_charge | Set total charge ]]
## [[CrocoBLAST:Job_management#JobSetup#BLASToptions | BLAST options]]
## [[ChargeCalculator:Job_submission#Pick_EEM_parameters | Pick EEM parameters ]]
# [[CrocoBLAST:Job_management#JobMonitoring | Job monitoring ]]
## [[ChargeCalculator:Job_submission#Pick_computation_method | Pick computation method ]]
# [[CrocoBLAST:Job_management#QueueAdministration | Queue administration ]]
# [[ChargeCalculator:Job_submission#Start_computation | Start computation ]]
 
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===[[ChargeCalculator:Interpretation_of_results | Interpretation of results]]===
===[[CrocoBLAST:Interpretation_of_results | Interpretation of results]]===
# [[ChargeCalculator:Interpretation_of_results#Synopsis_page | Synopsis page ]]
 
# [[ChargeCalculator:Interpretation_of_results#Specifics_page | Specifics page ]]
## [[ChargeCalculator:Interpretation_of_results#Summary | Summary ]]
## [[ChargeCalculator:Interpretation_of_results#Raw_data | Raw Data ]]
## [[ChargeCalculator:Interpretation_of_results#Analyze | Analyze ]]
## [[ChargeCalculator:Interpretation_of_results#Compare | Compare ]]
## [[ChargeCalculator:Interpretation_of_results#3D_model | 3D Model ]]
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===[[ChargeCalculator:Case_studies | Case studies]]===
===[[CrocoBLAST:Case_studies | Case studies]]===
# [[ChargeCalculator:Case_studies#Paracetamol | Paracetamol]]
# [[CrocoBLAST:Case_studies#EcoliProteome | E. coli proteome]]
# [[ChargeCalculator:Case_studies#Apoptosis | Apoptosis]]
# [[CrocoBLAST:Case_studies#ScerevisiaeWGS | S. cerevisiae whole genome sequencing data]]
# [[ChargeCalculator:Case_studies#Proteasome | Proteasome]]
# [[CrocoBLAST:Case_studies#HMPmetagenome | Human Microbiome Project metagenome sample]]
# [[CrocoBLAST:Case_studies#HMP16S | Human Microbiome Project 16S genome sample]]


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===[[ChargeCalculator:Technical_details | Technical details ]]===
===[[CrocoBLAST:Technical_details | Technical details ]]===
# [[ChargeCalculator:Technical_details#Requirements | Requirements]]
# [[CrocoBLAST:Technical_details#Requirements | Requirements]]
# [[ChargeCalculator:Technical_details#Limitations_and_troubleshooting | Limitations and troubleshooting]]
# [[CrocoBLAST:Technical_details#Limitations_and_troubleshooting | Limitations and troubleshooting]]


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===[[ChargeCalculator:Theoretical_background | Theoretical background ]]===
===[[CrocoBLAST:Theoretical_background | Theoretical background ]]===
# [[ChargeCalculator:Theoretical_background#EEM | EEM ]]
# [[CrocoBLAST:Theoretical_background#Alignment | Local alignment algorithms ]]
# [[ChargeCalculator:Theoretical_background#EEM_Cutoff | EEM Cutoff ]]
# [[CrocoBLAST:Theoretical_background#BLAST | BLAST programs]]
# [[ChargeCalculator:Theoretical_background#EEM_Cutoff_Cover | EEM Cutoff Cover ]]


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===[[ChargeCalculator:Index | Index ]]===
===[[CrocoBLAST:Index | Index ]]===

Revision as of 10:28, 21 July 2016


Below you can find the CrocoBLAST user manual, which contains all the information you need in order to make efficient use of CrocoBLAST. Note that you need not install CrocoBLAST, as it is sufficient to download the files from the webpage and unzip them. You may run CrocoBLAST from the graphical interface or directly from the command line. Using the graphical interface currently requires Java - but don't worry, you probably have it already. If you get in trouble, see the Technical details page.

Happy sequence munching! Nom nom!

What can I do with CrocoBLAST?

Frequently Asked Questions

Introduction

Terminology:

  1. Database
  2. Job
  3. Queue

Job management

  1. Job setup
    1. CrocoBLAST options
    2. BLAST options
  2. Job monitoring
  3. Queue administration

Interpretation of results

Case studies

  1. E. coli proteome
  2. S. cerevisiae whole genome sequencing data
  3. Human Microbiome Project metagenome sample
  4. Human Microbiome Project 16S genome sample

Technical details

  1. Requirements
  2. Limitations and troubleshooting

Theoretical background

  1. Local alignment algorithms
  2. BLAST programs

Index

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