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APPENDIX II - Alphabetical list of scanps commands

This section is simply a sorted and extended version of the scanps_alias.dat file. New commands may from time to time get added to that file, so look there if something does not makes sense.

APPLY_INDEX     apply_index	

Flag when creating database in mode 99 if =1 then the characters used
to represent the amino acids in the binary sequence database are
converted to allow fast indexing of the pairscore matrix.  This is the
default.  If you use a lot of different pairscore matrices with
different index strings, then set this to zero.

APRINT_TO_THRESHOLD aprint_to_threshold aptt  

Flag to specify if alignments will be printed down to the probability
threshold defined by PROBCUT.

AUTO_CORNER	auto_corner	# Obsolete

BDB_ROOT	bdb_root	bdb     

Name of root name for binary database files - e.g. sprot would mean
there is a file called sprot.bix and sprot.bsq.

BLOCK_FILE_OUT block_file_out  bfo 

Name for a file to contain multiple alignment output in AMPS block file format.

CALEB_LPLBUCKETWIDTH buckwidth  # logprodlen bucket width
CALEB_MINBUCK   minbuck         # minimum number needed for a stats bucket.
CALEB_MINRANGE  minrange        # minimum number of buckets needed for fitting.
CALEB_PRINT     caleb_print     # print out the caleb stats files.  1 = yes, 0 = no.

Options related to the Webber and Barton on-the-fly statistics.

CODON_FILE	codon_file	#Translation table for DNA to Protein

COMPLEMENT_QUERY comp_query	cq # scan with complement of DNA query	

CUT_CONSTANT	cut_constant	# Obsolete
CUT_CORNERS	cut_corners	# Obsolete

DB_DIR		db_dir		

Directory for storing database files.

DB_FILE		db_file 	d	

Sequence database filename - name for file that is not a binary database file.

DB_FORMAT	DB_F		db_format	dbf	 

As for QSEQ_FORMAT - the format of the database sequence.

DO_SORT	     	do_sort	        # Obsolete.

DO_STATS	do_stats	

This should always be set to 2.

DUMP_STATS      dump_stats      # Obsolete.

EPB_PEN		epb_pen		# Obsolete.
EPL_PEN		epl_pen		# Obsolete.
EPR_PEN		epr_pen		# Obsolete.
EPT_PEN		ept_pen		# Obsolete.

EXTRACT_FILE	extract_file	efile	# Obsolete.
EXTRACT_SEQ	extract_seq	eseq	# Obsolete.
EXTRACT_SEQ_FORMAT	extract_seq_format	# Obsolete.

FAST            fast            # Obsolete.
FIND_REPEATS	find_repeats	# Obsolete.

FIT_FILE	fit_file	# Obsolete.
FIT_TYPE        fit_type        # Obsolete.

FRAG_FILE_FORMAT frag_file_format fff 

Format of the frag file optionally output for a profile alignment 0
for PIR 1 for FASTA.

FRAG_FILE_OUT frag_file_out  ffo # the name of the frag file to output

FSE_PEN		fse_pen		# Obsolete.
FS_PEN		fs_pen	FSC_PEN	fsc_pen	

Penalty for frame shift creation in DNA vs Protein modes.

GAP_CHARACTER	GAP_CHAR	gap_character	gap_char

Character used to show a gap.

GENERAL_DIR	gen_dir		

Directory to store miscellaneous information in - e.g. the codon.dat file.

LD_PEN		ld_pen	e_pen	E_PEN		

Length dependent (extension) gap penalty

LICENSE_DIR     license_dir     # Obsolete.

LI_PEN		li_pen	c_pen	C_PEN

Length independent (creation) gap penalty

LOG_SCORES	log_scores	lns	# Obsolete.

MATRIX_DIR	matrix_dir	md 

Directory that contains pairscore matrices.

MATRIX_FILE	matrix_file m	

Name of pairscore matrix file.

MATRIX_FORMAT	matrix_format	mf	

Format of matrix file =0 for PIR =1 for NCBI/BLAST

MAX_AOUT	max_aout	maout	

Max number of alignments to output - works in conjunction with -aptt option.

MAX_BLOC_SEQ	max_bloc_seq	max_blc_seq	# Not used.

MAX_ID_LEN	max_id_len	

Maximum length for sequence identifiers

MAX_NOUT	max_nout	mnout	

Max number of sequences to output in score list (works with -nptt).

MAX_NSEQ	max_nseq	

Maximum number of sequences allowed in program - this must be bigger than the database size.

MAX_SEQ_LEN	max_seq_len	

Max allowed length for an amino acid sequence.  In most compiled programs this has
a precompiled limit.  If the program is compiled without MMX/SSE support or parallel
processing support, then this variable can be set.

MAX_TITLE_LEN	max_title_len	#Maximum length for sequence titles

MIN_ASCORE	min_ascore	# Obsolete.

MIN_LEN		min_len		# Minimum length allowed for an alignment

MIN_NSTATS	min_nstats	# Obsolete.

MIN_SCORE	min_score	# Minimum score required for score list to be output

MIXED_MODE mixed_mode mm        # 

When set to 1 and mode 202 is active, first iteration is mode 202
others are mode 200.

MM_LD_PEN  mm_ld_pen  mmpen     

Length dependent penalty to use in MIXED_MODE on iterations 1-N

MODE		mode

Specify type of scan or processing - see manual above.

MULTIPLE_OUTPUT_LENGTH	multiple_output_length	mol 

Output length for multiple alignments

NCHUNK nchunk 

MPI chunk size - number of sequences to send to each processor in each
parallel chunk.

NITER		niter

Number of iterations to do.

NPRINT_TO_THRESHOLD nprint_to_threshold nptt  

If 1 then output is down to probcut threshold if 0 then MAX_NOUT is

NRANS		nrans		# Obsolete.

OSEQ_FILE	oseq_file	# Obsolete.

OUTPUT_LENGTH	output_length	out_len	OUT_LEN 

Output length for pairwise alignments.

PCUT		pcut		# Obsolete.

PEN_FACTOR pen_factor penf

Factor to modify observed gap penalties in modes 210/212

PIDTHRESH pidthresh pidt        

percentage identity threshold for inclusion in profile.

POSWGTFAC poswgtfac pwf		# profile position specific weighting factor

PRECISION	precision 	precis	PRECIS	

Precision - all floats multiplied by this number.  Usually 100.

PRED_FILE	pred_file	# Obsolete.

PRINT_ALIGN	print_align	# Obsolete.

PRINT_BLOCK_FILE print_block_file pbf 

If 1 then will print an AMPS block file for the multiple alignment.

PRINT_FRAG_FILE print_frag_file pff 

If 1 then will print a file of seq fragments in format.  See manual.

PRINT_FRQ_TABS  print_frq_tabs  

Print out the frequency tables in an iterated search.

PRINT_PROFILES  print_profiles  

Print out the lookup tables in iterated search.

PROBCUT	        probcut         eval 

Probability or eval cutoff for do_stats 1 or 2.

PROBCUT2	probcut2         eval2 

Probability or eval cutoff for inclusion in profile.

PROB_TYPE prob_type             

prob type 0=probs 1 =oldevals 2 =newevals - only prob_type 2 is tested.

PROFILE_WEIGHT_METHOD profile_weight_method pwm 

0 for original weighting 1 for HH.

QBLC_FILE	qblc_file	QBLC	# Obsolete.

QBLC_FORMAT	QBLC_F		qblc_format	# Obsolete.

QSEQ_FILE	qseq_file	QSEQ	qseq	s	S

Query sequence file.

QSEQ_FORMAT	QSEQ_F		qseq_format	qsf	 

0 = PIR format, 1 = FASTA format

READ_PRED	read_pred 	# Obsolete.
ROBSIM		robsim 		# Obsolete.
RUN_SW_MIN	run_sw_min	# Threshold required before NALL algorithm runs

SAVE_PROFILES	save_profiles	# Obsolete.
SCAN		scan		# Obsolete.
SEC_FILE	sec_file	# Obsolete.
SHOW_BLURB      show_blurb      

If set to 0 then no info is printed to output file.

SHOW_IDENT_WIDTH	show_ident_width	siw	

The width of the ident string to output.

SHOW_LEN	show_len	lens	# Obsolete.

SHOW_PMATRIX 	show_pmatrix	spm	

Print pairscore matrix to output file (requires SHOW_BLURB).

SHOW_TITLES	show_titles	titles	

Print titles in output.

SHOW_TITLES_WIDTH	show_titles_width	stw

The width of the title string to output.

SPECIAL		special		# Obsolete.

STDERR		stderr		# redefinition of stderr
STDIN		stdin		# redefinition of stdin
STDOUT		stdout		# redefinition of stdout

STOP_WEIGHT	stop_weight	sw  # 

Weight for matching amino acid to STOP codon (MODE 22).

TEST #Test - no alias

TIME		time		# Set to 1 to record CPU times

TOP_CUTFRAC     top_cutfrac     # Obsolete.
TOP_ONLY	top_only	

1 for only top scoring alignment in each pair. 0 for all alignments
down to probcut.

USE_GAPDEFS     use_gapdefs     ugd  

if = 1 then use scanps_Gapdefs.dat values if posssible

VERBOSE		verbose		

If >=1 then print various messages as program runs.

VINGRON_FILE	vingron_file	# Obsolete.

Geoff Barton (GJB) 2002-07-23