Tracking Down Reference Database For Alignment

Question

[blake.mcmurray]

Hello,

I have been tasked with tracking down 16s references from a species of hotspring cyanobacteria for use in running an alignment, but have found the process difficult. The resources I have been instructed to check are:

JGI NCBI RDP SILVA

My question is, for anyone who may have experience doing this kind of work (manually finding large amounts of specific fasta files) is there any advice you would give? Do these websites provide tutorials of how to search their databases that can be read or viewed on YouTube? Apologies if this question is amateur, but I am an amateur...

Kind regards,

Blake

Answer 1

[GenoMax]

NCBI Tutorials can be found here: https://www.ncbi.nlm.nih.gov/home/tutorials/ . Check for "search" term
RDP had tutorial here: https://rdp.cme.msu.edu/help/tutorial.jsp
SILVA tutorial is here: https://www.arb-silva.de/documentation/search-tutorial/
JGI is here: https://genome.jgi.doe.gov/portal/ It will require time to create an account and then look around the site.

There are tutorial on YouTube for perhaps all these. They may be of variable quality. Use at your discretion.

[blake.mcmurray]

Thank you very much.