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Table 3 Examples of GLUE module types

From: GLUE: a flexible software system for virus sequence data

Module type Description
fastaProteinAlignmentExporter Creates amino-acid level alignments from Alignments within the GLUE project. A protein-coding FeatureLocation is specified along with a set of AlignmentMember objects selected from a given Alignment and its descendents. A translated amino-acid alignment is generated based on the stored homologies for the selected member sequences, which can then be exported to a file or used in further computation.
blastProteinFastaAlignmentImporter Imports amino-acid level alignments into the GLUE project to be stored as nucleotide alignments. For each row of this input alignment a GLUE Sequence object is identified. TBLASTN is used to compare the alignment row with the nucleotides of the identified sequence. In this way, the nucleotide-level homologies implicit in the file are identified and AlignedSegment objects representing this homology are created within an unconstrained GLUE Alignment.
ncbiImporter Runs an eSearch query on the GenBank database [26, 27], based on a configurable search term. Records are downloaded in GenBank XML format and stored as GLUE Sequence objects.
genbankXmlPopulator Operates on a set of Sequence objects which are stored in GenBank XML format. According to configurable rules, it extracts data items from the GenBank XML, executes transformations on them and updates auxiliary data fields or associations on the corresponding Sequence object.
samReporter Provides functionality for interpreting SAM/BAM files [28] containing high throughput sequencing data. One example is the amino-acid command, which will translate those reads in the file which map to a specific protein-coding feature in the project. The command outputs the proportions of amino acid residues found at each location.