I have a batch of fasta files, each one is a file of ESTs from a different plant. I want to create a database for all the plants, how can I use formatdb (or another way) to create one database which I could blast against?
formatdb accepts stdin for the argument -i . See the manual.
This parameter is mandatory. It requires the full file name with extension. The input file should have sequences in FASTA or ASN.1 format, except when converting a gi list to binary form. To format multiple input files, quote the input file names as in -i "db1 db2". The FASTA output from other programs can be pipe to this option using "-i stdin". Renaming of database is recommended (mandatory in the first case).
So, using unix find, you can do something like this:
Make all your fasta sequence in a single text file. remember to use single gap between all sequences.Then give a file name in extension .txt. suppose your input file name is abc.txt which contain all the ESTs. then use the following command for formatting.