assembleByProtv2.pl updated to run with blastx

assembleByProtv2.pl now calls blastx with 4 threads. Created blast
database is now named in the config file.

Updates to legacy blast programs:
    blastall has been replaced with blastx from the blast+ suite.
    formatdb is replaced with makeblastdb.

Removed job_ files from SGE and added to .gitignore.

Moved README back to outer level where Github wants it.