I'm having a bit of trouble with searching for this piece of information. I'm doing a study related to phylogenetic susceptibility of hosts to pathogens (based on a recent Nature publication), specifically to flu. This requires knowing the reference 18S ribosomal DNA sequence for chickens, wild ducks, horses, pigs and humans (amongst others). Is there a resource that enables us to easily download these?
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$\begingroup$ I presume you have tried the usual sources (NCBI, ensembl etc ?) $\endgroup$– Rover EyeCommented Apr 27, 2015 at 23:25
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$\begingroup$ Yes, I have tried the usual sources, my biggest question was whether they had a "reference" genomic 18S rDNA sequence, or if the NCBI sequences themselves were reference sequences. $\endgroup$– ericmjlCommented Apr 27, 2015 at 23:55
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1$\begingroup$ Considering the chicken is sequenced, I'd say that its the same thing. tbh I am not too sure of what exactly you ant, but for ll intent and purposes, you'll be using the sequences from below for your analyses $\endgroup$– Rover EyeCommented Apr 28, 2015 at 7:40
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2 Answers
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For birds you can start by searching 18s in http://birdgenenames.org/cgnc/
But generally NCBI Nucleotide database, should provide you with all information and accession numbers. See this broad search: http://www.ncbi.nlm.nih.gov/nuccore/?term=18S+ribosomal+RNA+gene
Adding species specification and other parameters, you might find what you are looking for. For example, see chicken 18S ribosomal RNA gene
answered Apr 27, 2015 at 23:29
aaaaa says reinstate Monicaaaaaa says reinstate Monica
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I may be jumping the gun here, but assuming that you haven't searched NCBI or ensembl, I'd do that first.
Essentially all genomic information is maintained by a collaboration between US NIH, EU EBI and Japan. All databases are synced to each other, and hence the data should (theoretically) be the same (in practice it never is). I'd suggest you pick one server and stick to it.
In my lab we prefer to use NCBI, but that differs from lab to lab.
You can search NCBI by following the tutorial here (http://www.ncbi.nlm.nih.gov/guide/howto/find-published-info-gene-sequence/) or ensembl bu following the tutorial here (http://www.ebi.ac.uk/training/online/course/ensembl-browsing-chordate-genomes/how-search-ensembl)
A sample search for chicken gives you this (http://www.ncbi.nlm.nih.gov/gene/100861561) with three entries for genomic dna and one for mRNA. I'd choose a complete sequence over a partial sequence.
You might also want to look up in their help the meaning of cds (coding sequence; you'll encounter it)
