My group investigates a family of proteins. We need to get all members of this family which are in NR database. In the past, my colleagues made it by 5 iterations of psi-blast against NR. This data is outdated and now and we need to renew it.
My question is general. Is it possible to make all this by psi-blast from blast+ without downloading the whole nr on a server? It seems to me that the user can't define several options when using ncbi severs. Do I understand right that the only way to solve this problem is to download nr and make all manipulations on a local server? Thanks :)