This might be a basic question but I am wondering how does one approach this task? My aim is to compare specific genes from the published genomes of the closest sequenced species/genera to my organism.
I was surprised at first and asked if I will make a similar database as BLAST but I was told that by "database" they expect me to just download FASTA files from Genbank. Is that simply it?
Thanks!
Hi Angelo,
Do you mean you want to make a local database with your organism and closest relative with some specific genes ? If so, you can download all the desired set of genes and can make a local BLAST database. You can use this database similar to the blast database. The benefit of such database can be the speed of search and size of resulting file will be small. It could give better results of one or similar kind of genes as there less chances of similar hits in blast search
I recommend you the KEGG database (http://www.genome.jp/kegg/). There you find the complete genomes available to date. In this list you find them phylogenetically ordered: http://www.genome.jp/kegg/catalog/org_list.html
If you do not have an active subscription it can be a little complicated to download the genomes, but nothing impossible with a script (although paying the subscription is highly recommended).
Once you have the genomes you want, you can build your database with the BLAST commands, and then perform your analysis.