Problems with using WebACT to create crunch files for ACT

Question

[dadarotimi]

I have been trying to create crunch files of two prokaryotic genome so I can compare both genomes using Artemis Comparison Tool (ACT). However, all my effort has been unsuccessful. I do not get any e-mail confirming that I have submitted a request or that my request has been processed. All I get whenever I use the link for my query is:

WebACT | Running Query WebACT Status You can either wait for the comparison to complete, or bookmark this link and return at a later date Results will be retained on the server for 7 days

I'll appreciate if anyone can help.

Thank you in advance.

[vlancl1]

Did you ever get your results? If so, how long did it take? I've submitted mine about 1.5 hours ago and didn't get a link or email either. My genomes are very small, so I wouldn't expect the program to have any issues with them.

Answer 1

[dadarotimi]

Vlancl1, I eventually got a way out the mess created by WebAct and DoubleAct- In a terminal, I typed the following:

1. sudo apt-get install ncbi-blast+ (to downloaded Blast)

2. makeblastdb -in Genome1 -dbtype nucl

3. blastn -query genome2 -db Genome1 -evalue 1 -task megablast -outfmt 6 > Genome1_Genome2.crunch

make sure you have the assembled genome that you want to compare in your working directory

PS: Kathryn Holt helped me with the paper she co-authored - https://katholtlab.files.wordpress.com/2017/07/comparativegenomicstutorialv2.pdf