We have a series of posts about crAssphage. Enjoy them!
Category Archives: Lab blog
Similarity Searching the SRA
The NCBI SRA contains a lot of data – about 1016 bp at the moment! However, searching that has always been problematic. We’re happy to unveil a new search SRA service that allows you to search the random metagenomes in the SRA using either DNA or protein queries.
Phage Gene Callers
Which phage gene callers are people using?
We are curious how people annotate their phage genomes, and so we looked at both the genbank records and the literature.
Install Anvi’o on an AWS Instance
We wanted to use Anvi’o on a windows machine, but that is impossible, so we set up an AWS free instance with anvi’o 5 up and running for the windows users. Here’s how to do it.
How to mess with BLAST results
Running Mauve with Java 10
They short answer is you can’t (currently) run the totally awesome Mauve with Java 10, but you can probably run Mauve anyway. Here’s how!
TL;DR
locate java | grep java$ | grep -w bin export JAVA_CMD=/usr/lib/jvm/java-8-openjdk-amd64/bin/java
phage terminase orientation
I was recently looking at the relative orientation of phage terminase genes along the genome. Here is a little summary.
Downloading all the sequences from a PATRIC family
PATRIC families are somehow organized sets proteins that are related. Sometimes we want to get all the protein sequences in the family. Here’s how to do that using the PATRIC command line
Submitting a PATRIC genome annotation using the command line
The PATRIC BRC has a great command line interface that allows you to access much of the data remotely. Here is a simple recipe to submit a genome for annotation.
Teaching Bioinformatics
We teach a lot of bioinformatics. Here are some public resources we rely on. These are pulled from twitter, the web, and all over the place, and the text ended up being used elsewhere. Please feel free to suggest more to Rob!