Let's say I want to find the upstream sequence for ACTA1 for every species of, say, birds that have such data available. There are 45 whole bird genomes along with annotations available here. In total, there are around 50 bird species with genome assemblies available, but they don't seem to be all in one place. Anyway, how can one get the upstream sequence from some gene, say ACTA1, for all 45 species available on gigadb, or for all the birds available on some other database (e.g. NCBI has 28 species: go to http://www.ncbi.nlm.nih.gov/gene and search (ortholog_gene_58[group]) AND "birds"[porgn:__txid8782]).
I prefer answers that use the R programming language, but other approaches are welcome.
Genomes are available here
Thanks for pointing out another place where many (though not all) bird genomes are available!