Software Ensembl Core Database Schema Common Feature Tablesseq_region_id, seq_region_start, seq_region_end, seq_region_strand: sequence position of the alignment.
hit_name the name or primary id of the aligned sequence in the database, described in the associated analysis.
hit_start, hit_end, hit_strand: sequence position of the aligned stretch of DNA on the hit_name sequence.
score, evalue, perc_ident selected quality numbers for the alignment. The API supports score as a filter criterion.
cigar_line a string that describes the alignment. Pieces of matching sequence M, deleted bases D and inserted bases I.
Describes an alignment between an external peptide sequence and a piece of Ensembl DNA sequence. It is equivalent to the dna_align_feature table apart from:
there is no hit_strand as protein sequence cannot have a negative strand
the interpretation of the hit coordinates, as they are amino acid counts.
the cigar_string uses DNA basepair counts for the alignment description.
Repetitive regions on the genome are stored in this table. All repeats are further classified by the repeat_consensus table.
repeat_start, repeat_end and score are retrievable by the API but not used by it (the API cannot filter by this criteria). Repeats are retrievable by their different consensus sequence (type).
A prediction transcript is a gene prediction of low quality where there is not much information provided (compared to the information for a gene, see below). Prediction transcripts link to one or more prediction exons and an analysis, which generated this prediction (and the prediction exons).
rank The position of the exon, starting from 1, in the transcript from the 5 prime end.
start_phase describes whether the prediction exon starts with the first, second or third base in a codon.
The
