CrocoBLAST:UserManual

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!

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Terminology:

1. Input file and Database
2. BLAST program
3. BLAST options
4. Job
5. Queue

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Job management

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

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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

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Technical details

1. Requirements
2. Limitations and troubleshooting

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Theoretical background

1. Local alignment algorithms
2. BLAST programs

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