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Sorry if this seems like a naive and simple question. I have the whole genome of my species as a fasta file and a file containing a list of protein IDs. What is the easiest way to get a file that contains the fasta sequence for each of the proteins in the second file?
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What species?
If it is one of the common genomes NCBI is likely to have the protein fasta file available. -
I can get the protein fasta file. It's more the extracting the sequence for my specific list of protein IDs that I'm struggling with.
It is the monarch butterfly so not a particularly common species.Comment
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Look into faSomeRecords utility from Jim Kent: http://hgdownload.soe.ucsc.edu/admin.../faSomeRecords I have provided linux link but OS X/Source code is also available at the site.
Provide the list of ID's to faSomeRecords and it will extract the fasta sequence for your ID's, which you can save to a new file.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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