Contains all settings. More...
#include <structs.h>
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 |
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().
char* gotoh_settings::dbase |
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
float gotoh_settings::m1_seqT |
Sequence threshold to be a matching pattern for single motifs. Default: 0.7
float gotoh_settings::m2_seqT |
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
float gotoh_settings::m2T |
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
char* gotoh_settings::motif1 |
Filename of query file containing a motif as frequency matrix reformatted using scripts/reformatFasta.pl
char* gotoh_settings::motif2 |
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 sequencesDefault: 0
float gotoh_settings::percID |
Percent identity - only candidate alignments with higher or equal percent identity than this value are returned. Default: 60
char* gotoh_settings::query |
Filename of query file conatining FASTA formatted (ungapped) sequences.
char* gotoh_settings::res_file |
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
double gotoh_settings::usrE |
Evalue - only candidate alignments with lower or equal Evalue than this value are returned. Default: 1e-3
Print Verbose output.