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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

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DESCRIPTION

Sequence alignment hits were previously stored within the core database as ungapped alignments. This imposed 2 major constraints on alignments:

a) alignments for a single hit record would require multiple rows in
   the database, and
b) it was not possible to accurately retrieve the exact original alignment.

Therefore, in the new branch sequence alignments are now stored as ungapped alignments in the cigar line format (where CIGAR stands for Concise Idiosyncratic Gapped Alignment Report).

In the cigar line format alignments are sotred as follows:

M: Match
D: Deletino
I: Insertion

An example of an alignment for a hypthetical protein match is shown below:

Query:   42 PGPAGLP----GSVGLQGPRGLRGPLP-GPLGPPL...
            PG    P    G     GP   R      PLGP
Sbjct: 1672 PGTP*TPLVPLGPWVPLGPSSPR--LPSGPLGPTD...

protein_align_feature table as the following cigar line:

7M4D12M2I2MD7M