Editing DNA sequencing

Jump to navigation Jump to search

Warning: You are not logged in. Your IP address will be publicly visible if you make any edits. If you log in or create an account, your edits will be attributed to your username, along with other benefits.

The edit can be undone. Please check the comparison below to verify that this is what you want to do, and then publish the changes below to finish undoing the edit.

Latest revision Your text
Line 12: Line 12:
   
 
How to upload DNA sequences to Genbank: https://www.facebook.com/groups/FungalSequencing/permalink/2163215977233131/
 
How to upload DNA sequences to Genbank: https://www.facebook.com/groups/FungalSequencing/permalink/2163215977233131/
 
Jerry Cooper's excellent Notes on home-based PCR for barcoding fungi: https://www.funnz.org.nz/sites/default/files/DIY%20DNA%20PCR_2.pdf
 
   
 
== DNA Extraction ==
 
== DNA Extraction ==
Line 26: Line 24:
   
 
[[http://i.imgur.com/9fLgFqJ.jpg|thumb|left|alt=NaOH DNA Extraction]]
 
[[http://i.imgur.com/9fLgFqJ.jpg|thumb|left|alt=NaOH DNA Extraction]]
 
Another good way to extract DNA is with IBI X-Amp. PCR success is as good or better than the other methods, and there's not as much that can be messed up since you don't need to mix any chemicals. https://www.ibisci.com/products/x-amp-dna-reagent
 
 
   
   
Line 113: Line 108:
 
* Use the FASTA file to build a phylogenetic tree using [http://www.megasoftware.net Mega 7] for Windows, [http://ugene.net uGene] for Linux or the more difficult but powerful multiplatform command line tool [http://sco.h-its.org/exelixis/web/software/raxml/index.html RaxML] and the java program [http://tree.bio.ed.ac.uk/software/figtree FigTree] to visualize the tree. The easiest way to make a tree is to use the one-click mode at [http://phylogeny.lirmm.fr http://phylogeny.lirmm.fr] - this website allows you to upload a FASTA file, aligns the sequences and makes a tree using the [https://en.wikipedia.org/wiki/Maximum_likelihood Maximum Likelihood] algorithm.
 
* Use the FASTA file to build a phylogenetic tree using [http://www.megasoftware.net Mega 7] for Windows, [http://ugene.net uGene] for Linux or the more difficult but powerful multiplatform command line tool [http://sco.h-its.org/exelixis/web/software/raxml/index.html RaxML] and the java program [http://tree.bio.ed.ac.uk/software/figtree FigTree] to visualize the tree. The easiest way to make a tree is to use the one-click mode at [http://phylogeny.lirmm.fr http://phylogeny.lirmm.fr] - this website allows you to upload a FASTA file, aligns the sequences and makes a tree using the [https://en.wikipedia.org/wiki/Maximum_likelihood Maximum Likelihood] algorithm.
 
*For more professional phylogenetic trees, use RaxML or MrBayes to generate the tree, then visualize it with Figtree.
 
*For more professional phylogenetic trees, use RaxML or MrBayes to generate the tree, then visualize it with Figtree.
* Seqtrace is a free program developed by Google which can generate a consensus sequence from forward and reverse chromatograms.
 
   
 
[http://asserttrue.blogspot.com/2014/05/how-to-build-your-own-phylo-trees-with.html How to use Mega on Windows to make phylogenetic trees]
 
[http://asserttrue.blogspot.com/2014/05/how-to-build-your-own-phylo-trees-with.html How to use Mega on Windows to make phylogenetic trees]

Please note that all contributions to Counter Culture Labs are considered to be released under the Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0) (see Counter Culture Labs:Copyrights for details). If you do not want your writing to be edited mercilessly and redistributed at will, then do not submit it here.
You are also promising us that you wrote this yourself, or copied it from a public domain or similar free resource. Do not submit copyrighted work without permission!

Cancel Editing help (opens in new window)