I want to extract the differences from two versions of one blast database. I am using php to do this task. first, i extract gi number only from each version using blastdbcmd. then, i do unix join that find the differences between the two gi files. then, i write while loop to read each gi from one file and extract the sequence for that gi using blastdbcmd. implementing these steps will generate a text file that contain the newly added sequences.
I read something about fadiff which extract the difference from fasta files. I want to know how to run this tool? it seems that it will replace my long processes in one line.
can anyone help me please?