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General: Searching and opening documents without browsing folder contents
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Jul 29th 2010
I have imported two isotig.fna files from a 454 transcriptome sequence runs to Geneious. Each contains c. 20000 isotigs ranging from 50 to c. 20000 bp. Most are around 500-1000. The features of Geneious are great for my needs, but it seems like there are major memory issues, causing the software to slow down consideably. I am using Geneious 5.0.4 on a MacBook Pro running Mac Os X 10.6.4, 2 Gb RAM and Intel Core 2 Duo 2.16 GHz processor. It takes a LONG time to load the isotig files the first time the folder is opened, and after that everything becomes really slow. Maybe there is a better workflow? What I do basically is that I BLAST a sequence againt the transcriptome database, get a match, and then I want to lookup the isotig. Is there a more efficient way to do this other than browsing the folder with the 20000 isotigs? For example, is there a way to search for a document by name, and then open it without having to browse the entire flder contents?
Jul 29th 2010
Unfortunately for this sort of work, 2GB isn't enough which is why your machine is thrashing. We're working to make Geneious more memory efficient all the time but that is a lot of documents.
Shane
Shane
Jul 29th 2010
Yes you can find a document by name without needing to open the entire folder. Click on the top level folder (called "Local"). Click on the search button in the top right corner and type in the name of the document you want to find in the search box that appears below it.
Alternatively rather than importing all your sequences as stand-alone documents, when you import them you can choose to import them into a single sequence list document. This will significantly improve performance and reduce memory usage.
It's not clear from your message, but if you intend to blast all 20,000 sequences using Geneious, I'd wouldn't recommend doing that as the current version of Geneious won't handle it well. We hope to improve that in future versions.
Alternatively rather than importing all your sequences as stand-alone documents, when you import them you can choose to import them into a single sequence list document. This will significantly improve performance and reduce memory usage.
It's not clear from your message, but if you intend to blast all 20,000 sequences using Geneious, I'd wouldn't recommend doing that as the current version of Geneious won't handle it well. We hope to improve that in future versions.
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