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Are there any tools available which will look at reference sequence and list out all the possible locations that can be potentially genes? or alternatively is there a tool that can take a sequence as input and predict if it can be a gene?
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I think you are really talking about 'ab initio' gene prediction (see https://en.wikipedia.org/wiki/Gene_prediction) and there are a lot of tools that can do this.
Maybe Maker could be useful to you: http://www.yandell-lab.org/software/maker.html -
kbradnam, Thanks a ton for this real quick reply.. This is exactly what I am looking for. Has anyone run these tools on entire human reference say hg18 or hg19?Originally posted by kbradnam View PostComment
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Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.
There is no single reason why many patients don’t respond to treatment as expected. Cancer is...Yesterday, 05:17 AM -
Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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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...
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