Public Attributes

gotoh_aln Struct Reference

Stores information about one alignment. More...

#include <structs.h>

List of all members.

Public Attributes

int db_len
char * hitseq
char * queryseq
char * hitname
char * queryname
int shift
int sStart
int sEnd
int length
char strand
float alnscore
float ntfalnscore
double evalue
float percID
int mismatches
int gapopening
int qStart
int qEnd

Detailed Description

Stores information about one alignment.

gotoh_aln contains all information about a single alignment. Alignment scores and positions in the database are computed during the forward recursion, while the alignment is obtained in the backward recursion. The E-value is calculated only after the complete set of database sequences has been scanned.


Member Data Documentation

Alignment score

Length of complete database sequence -> for maf output

E-value for alignment score

Number of gap opening events

Name of database entry

Aligned database (hit) sequence (with gaps)

Length of alignment

Number of mismatching pairs of bases

Unshifted (real) alignment score

Percent identity. Number of real matches vs. number of maximal possible matches

End of alignment in query. Should always be sizeof(query) due to global alignment

Start of alignment in query. Should always be 0 due to global alignment

Name of query sequence/pattern

Aligned query sequence/pattern (with gaps)

End position in database entry

Score to shift x-axis to zero

Start position in database entry

Strand of hit in database


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