Hi guys! I wonder how to find if some species/genera contain a specific gene. I have some human gut microbiome data derived from human faeces. The data includes gene abundance in each sample (each sample is faeces from each individual), taxonomy abundance in each sample (family, phylum, kingdom, genera, species). There is a gene that I am interested in, and I want to figure out what species/genera in our study contain this gene. There are hundreds of species detected, so I wonder if there is any program or any protocols that are routinely used for this purpose.
Thank you for your help in advance!
Is the data from metagenomic analysis or (your) gene-specific amplicon seq.?
If it is from gene-specific amplicon seq. then the answer is straightforward.
If it is a metagenomic analysis and you have the sequenced files/ assembled contig, then you need to quality BIN as many genomes as possible from the dataset (the cleaned sequenced Fastq files/assembled contig), annotate your bins, and can see which genome have your gene of interests. Though, you won't be able to get bins of all species.
Another method is using NCBI/DIAMOND BLAST on your sequenced Fastq files or if you have filtered gene sequence. A bit of coding can trace back the path of the annotated genome to the region it came from the original Fastq. Bioinformatics pipeline such as:
Squeezemeta https://github.com/jtamames/SqueezeMeta
SAMSA2 https://github.com/transcript/samsa2
have this functionality. But it is not guaranteed that it will trace back the path till species level. Secondly, this method is not reliable.
In any case, you won't be able to identify the functional genes in all detected species from a microbiome metagenomic dataset.
Близость – родство генов можно установить
Этот результат получается на математическом расчете
Метод позволяет выявить близкие виды
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