Resources for aspiring genomicists

Here is a brain-dump targeted at an incoming graduate student:

At some point, you should take a look at the following resources. They are very useful for any genomic analysis:

Reference Sequences from the National Center for Biotechnology Information (i.e. NCBI’s RefSeq)

Bacterial sequences

X. fastidiosa Temecula1

The most readable file is “.gbk”. Good for humans, bad for computers.

This file (README) describes the sequence formats

NCBI also has a convenient portal for all sequenced species, e.g. X. fastidiosa

Here’s a good system for getting information about genomes:

If you are going to do anything yourself, you should be familiar with BLAST (the best bioinformatic software ever made)
There’s the website for searching the general database:

…and the stand-alone package (BLAST+) which will be useful for looking at any new sequences we have:

Finally, useful GUI software for genome analysis:


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