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Hi I'm in need of some help. I need to find a motif with an ambiguous amino acid among sequences that range from 4 to 18 million long. I have a computer with 128 gb of RAM using Windows 7 and I've run motif searches with the programs CLC and Geneious, however, they take too long as they are very processor heavy. I initially tried blast, however, I found that blast does not do well with ambiguous amino acids. Any input would be greatly helpful!
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Try scan_for_matches:
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Thanks! However, after reading the instructions I found that it was CPU intensive not RAM intensive. Do you have any programs that runs primarily on RAM?
Thanks,
MinkyuComment
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Well, first all, all programs run in RAM. The issue is that those kinds of searches inherently are cpu intensive. It has nothing really to do with RAM. As long as you have enough RAM to load the search items and query string completely into RAM, then you have maximized your use of RAM and any limitation you experience is the result of computational effort.Originally posted by Minkyu View Post
The only thing you could do is run the search on a cluster, and partition the search items across multiple nodes (ie. each compute node only searches for a subset of the total sequences in your search set), so no one node has to bear the entire computational load.Michael Black, Ph.D.
ScitoVation LLC. RTP, N.C.Comment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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