Cross posted at StackExchange

https://bioinformatics.stackexchange.com/questions/11384/vegetable-databases-usage

It is generally unadvisable to cross post the same question in multiple communities, as it leads to duplication of effort.

You should add a lot more information here, because your question is wildly unclear.

However, in some cases we have meat mixed with vegetables and want only to detect the vegetable species

What are you working on? Do you really mean "meat", or perhaps "animal"?!

Do you have a list of target species and know if the genomes are available? If you have a list of vegetables with genomes available, you can index the genomes and use fastqscreen for initial contamination screen. You can also use any target genome indices and run against fastqscreen to know the contamination for first few sequences in the fastq or randomly chosen reads in the fasta (AFAIK).

C: Restricting database by taxa in local blast searches

As asked this question does not make sense. What do you mean by we have animal mixed with vegetables and want only to detect the vegetable species? There are many basic metabolism genes that would be common to animals/plants. I assume vegetable = plants?

How are you restricting your nt searches? My answer in this thread: A: blastx local terminal would be the way to restrict your blast+ searches.

What data do you have? Reads?

You could run it through Kraken or Centrifuge and have the reads classified. You can then just retain the ones which have Plantae hits. This isn't going to be fast though, even with a small-ish dataset.

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