Usage

Running the program

To run a compiled file blast in BLASTFAseed mode run with the parameter:

  -p blastp-seedfa
 

There is one more command line parameter: additional SeedBlast options are read from a config file:

 -x File to read a SeedFA extension configuration from. [String]
 default = seedfa.cfg
 

Example run:

 ./blast -p blastp-seedfa -x seedfa.cfg [TODO]

Config file options:

Allowed options in SeedFA config file (seedfa.cfg):

Example seedfa.cfg

-A [ --alignalph-file ] arg name of a file with the alignment alphabet
-S [ --seed-file ] arg name of a file with the alignment seed
-M [ --seed-file-homit ] arg shall the first line in the seed file be omitted flag
-K [ --seed-file-kind ] arg type of a seed-file 
  (0 - all hash values from the file;
   1 - all string descriptions from the file; log(P/Q) based choice:: 
   2- seedCount, 
   3- log(P/Q), 
   4- seedCover, 
   5- Pprob,
   6- Qprob; see manual for more info
   
--seed-file-param arg (=1) parameter threshold for log(P/Q) based choice of seeds (2-6)

Other parameters

A trade off between the time needed to construct a new query automaton and the memory needed to index queries can be adjusted using

batch_size

inside the file

  ncbi/demo/blast_driver.c

You need to recompile if changes are made.