Resources for aspiring genomicists

August 23, 2012 at 2:29 am · Filed under computers

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)
http://www.ncbi.nlm.nih.gov/RefSeq/

Bacterial sequences
ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/

X. fastidiosa Temecula1
ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Xylella_fastidiosa_Temecula1_uid57869/

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

This file (README) describes the sequence formats
ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/ReadMe.txt

NCBI also has a convenient portal for all sequenced species, e.g. X. fastidiosa
http://www.ncbi.nlm.nih.gov/genome/173

Here’s a good system for getting information about genomes:
http://www.microbesonline.org/

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:
http://blast.ncbi.nlm.nih.gov/Blast.cgi

…and the stand-alone package (BLAST+) which will be useful for looking at any new sequences we have:
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download

Finally, useful GUI software for genome analysis:
Mauve: http://gel.ahabs.wisc.edu/mauve/
Tablet: https://ngslib.i-med.ac.at/node/120

-adam

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