The query might seem silly to you but as a beginner, I need to learn and develop these new skills. Query: Suppose, I wish to download assemblies of Acinetobacter or say any other bacteria from NCBI, then, I simply enter the name (Acinetobacter or of other bacteria) in the search bar, do select assembly and gets some 11000 response. My problem is, I want to sort them i.e. sorting them according to their source of isolation. So, in totality, out of those 11000 responses, I just want the assemblies of acinetobacter that are isolated from insects or for that matter any insect i.e. Phylum Arthropoda or class insecta. So, is there a way out to do that or do I have to manually check each and every assembly to know about the source of its isolation.
Regards.. Neeti Pandey
@Neeti,
This is indeed an interesting albeit a difficult problem. There is no easy way to do this via the web search interface AFAIK. One gets very different numbers depending on where you look. In Genome section of NCBI website there seem to be about 6K genomes for all Aceinetobacter. Here that number jumps up to 11K (it includes all Aceinetobacter species). As soon as one add the "insects" term search results seem to go to zero. Entrezdirect is not very helpful either. What kind of insects (e.g. species names) would one look at?
You may want to put a help desk ticket in at NCBI to see if they can assist with a search on the backend database directly.
@genomax So..is there a way out for this particular problem or not....i actually want to have all the assembles of Acinetobacter but isolated from insects only and submitted to ncbi or any other databse