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From CDD readme
Has anyone experimented with different threshold values? 'Slightly increased' sounds rather vague..
The following sequence of commands will build the search databases:
makeprofiledb -title SMART.v6.0 -in Smart.pn -out Smart -threshold 9.82 -scale 100.0 -dbtype rps -index true
makeprofiledb -title Pfam.v.26.0 -in Pfam.pn -out Pfam -threshold 9.82 -scale 100.0 -dbtype rps -index true
..
Note that the parameter '-threshold' supplied with makeprofiledb, the three-letter
word score threshold for detecting and extending hits in RPS-Blast, will
determine the size of the search database. A lower threshold
will result in larger databases and slightly increased search sensitivity,
at the cost of additional memory requirements and reduced search speed.
Matrices distributed for creating RPS-Blast search databases are scaled by a
factor of 100 (parameter -scale). A score threshold value of 9.82 will result in
search-databases of a size very similar to using unscaled matrices and
a threshold value of 11.
makeprofiledb -title SMART.v6.0 -in Smart.pn -out Smart -threshold 9.82 -scale 100.0 -dbtype rps -index true
makeprofiledb -title Pfam.v.26.0 -in Pfam.pn -out Pfam -threshold 9.82 -scale 100.0 -dbtype rps -index true
..
Note that the parameter '-threshold' supplied with makeprofiledb, the three-letter
word score threshold for detecting and extending hits in RPS-Blast, will
determine the size of the search database. A lower threshold
will result in larger databases and slightly increased search sensitivity,
at the cost of additional memory requirements and reduced search speed.
Matrices distributed for creating RPS-Blast search databases are scaled by a
factor of 100 (parameter -scale). A score threshold value of 9.82 will result in
search-databases of a size very similar to using unscaled matrices and
a threshold value of 11.
