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NCBI/GenBank BLAST Output XML Parser Tool
see Blast 2.2.28
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This seems like a lot of unnecssary work now that BLAST itself offers descriptions in the tabular output,
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2.2.26 (2.2.27) didn't have this feature, and when I talked to NCBI they stated "no plans to include" - we wrote the script well over a year ago. I'm glad they did it.Originally posted by maubp View PostLast edited by cement_head; 08-20-2013, 01:55 AM.Comment
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I'd like to think my open letter blog post helped motivate them to add this
It wasn't clear from your post announcing your script that it pre-dated BLAST 2.2.28+ being released.Comment
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I was floored when I called them up and asked them why one couldn't extract that information with 2.2.26 - they said "why would anyone want to do that?" - so we wrote the script - anyway, thanks for pointing out that 2.2.28 does this (I hadn't checked).Originally posted by maubp View PostI'd like to think my open letter blog post helped motivate them to add this
It wasn't clear from your post announcing your script that it pre-dated BLAST 2.2.28+ being released.Comment
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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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