To generate PSSMs from tar zipped archive


In order to generate PSSMs(for Pfam domain families) for further use with RPS-BLAST:
Command line options for generating RPS-BLAST searchable database of families:
$ ls *.asnt > list.txt
$ ls *.chd > seqlist.txt
$ /BLAST/bin/formatrpsdb -i list.txt -n mydb
$ /BLAST/bin/formatdb -i seqlist.txt -n mydb


In order to generate PSSMs(for SCOP domain families) for further use with RPS-BLAST:
  • Download the zipped archive files for the desired domain families.
  • Each family has more than one profile with a ".chk" extension and the corresponding sequence files appended with a ".chd" extension.
  • A list of all *.chd files is required with ".sn" extension.
  • A list of all *.chk files with ".pn" extension. Ensure both lists have same name, but with different extensions
Command line options for generating RPS-BLAST searchable database of families:
$ ls *chk > database.pn
$ ls *chd > database.sn
$ /BLAST/bin/makemat -P database
$ /BLAST/bin/copymat -P database
$ /BLAST/bin/formatdb -i database



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