Molecular Basis of Bacterial Infections course, computer practical: References

After the practicum you will have some familiarity with working on the command line and will have a list of secreted proteins of two different species

You can use one set of log-in credentials for many instances

Logging off an instance is not the same as turning off an instance

The shell gives you the ability to work more efficiently by using keyboard commands rather than a GUI.

Useful commands for navigating your file system include: ls, pwd, and cd.

Most commands take options (flags) which begin with a -.

Tab completion can reduce errors from mistyping and make work more efficient in the shell.

The /, ~, and .. characters represent important navigational shortcuts.

Hidden files and directories start with . and can be viewed using ls -a.

Relative paths specify a location starting from the current location, while absolute paths specify a location from the root of the file system.

You can view file contents using less, cat, head or tail.

The commands cp, mv, and mkdir are useful for manipulating existing files and creating new directories.

You can view file permissions using ls -a and change permissions using chmod.

The history command and the up arrow on your keyboard can be used to repeat recently used commands.

grep is a powerful search tool with many options for customization.

>, >>, and | are different ways of redirecting output.

command > file redirects a command’s output to a file.

command >> file redirects a command’s output to a file without overwriting the existing contents of the file.

command_1 | command_2 redirects the output of the first command as input to the second command.

Sequencing data needs to be trimmed or corrected before use

Spend the time to organize your file system. Your future self will thank you!

Assembly is a process which aligns and merges fragments from a longer DNA sequence in order to reconstruct the original sequence.

k-mers are short fragments of DNA of length k

Genome annotation includes prediction of protein-coding genes, as well as other functional genome units

Annotation starts by identifying open reading frames

Predicted protein-coding sequences are further analysed with BLAST

Larger DNA sequences or genomes require automated prediction and annotation

Secreted proteins are predicted by identifying a signal peptide

The presence of a signal peptide does not necessarily mean that the protein is secreted

No matter which way you want to move data, it’s easier to start the transfer from your local machine

Computational predictions need to be validated by laboratory experiments