Public Attributes

gotoh_settings Struct Reference

Contains all settings. More...

#include <structs.h>

List of all members.

Public Attributes

char * dbase
char * query
char * res_file
char * motif1
char * motif2
int gap_open
int gap_extend
int match
int mismatch
int inf
int maxdistance
double usrE
float percID
float m1_seqT
float m2_seqT
float m2_strucT
float m2T
int output_format
char * stat_file
int verbose

Detailed Description

Contains all settings.

gotoh_settings contains all settings needed by GotohScan. Unset values are set to appropriate defaults. It can be initialized by gotoh_initSettings() and freed by gotoh_freeSettings().


Member Data Documentation

Filename of database file containing FASTA formatted sequences.

Penalty for extending an existing gap. Default: -2

Penalty for opening a gap. Default: -8

The definition of infinity which is used to initialize the scoring arrays of the Gotoh algorithm. Default: 999999

Sequence threshold to be a matching pattern for single motifs. Default: 0.7

Sequence threshold to be a matching pattern for 2-sided motifs. Default: 0.5

Structure threshold to be a matching pattern for 2-sided motifs. Default: 0.8

Complete Threshold for 2-sided motifs. Default: 0.6

Bonus for a matching pair of bases. Default: 3

Maximal distance between the 2 sides of the 2-sided motif

Penalty for a pair of bases that does not match. Default: -1

Filename of query file containing a motif as frequency matrix reformatted using scripts/reformatFasta.pl

Filename of query file containing a 2-sided motif as frequency matrices reformatted using scripts/reformatFasta.pl

Output format. Values are:

  • 0 - Blast tabular output
  • 1 - Blast tabular output + aligned sequences
  • 2 - FASTA format. NOTE: Hit sequence only, without gaps !
  • 3 - MAF format. NOTE: Header truncated to 30 characters!
  • 4 - BED + aligned sequences
  • 5 - GFF + aligned sequences

Default: 0

Percent identity - only candidate alignments with higher or equal percent identity than this value are returned. Default: 60

Filename of query file conatining FASTA formatted (ungapped) sequences.

filenmae of output file.

Filename of file where to statistics on the E-value calculation, i.e. the data of the histogram, the fit parameters and the final fitted curve

Evalue - only candidate alignments with lower or equal Evalue than this value are returned. Default: 1e-3

Print Verbose output.


The documentation for this struct was generated from the following file:
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