Sequence Explorer provides the visual representation of genome annotations. It works with files containing sequences in FASTA format and files with Fgenesh predictions for corresponding sequences, as well as with GenBank sequence annotation files.
Sequence Explorer allows visualization of many features such as CDS (protein coding regions), promoters, terminators, operon units, tRNA and rRNA genes predicted by MolQuest programs, as well as other features available from GenBank annotations.
It allows to visualize annotations for many sequences at the same time. This is convenient for visual comparing of annotations of different but related genomes, or for visual inspection of predictions in a set of sequences such as scaffolds of a bacterial genome or short reads of DNA extracted from a bacterial community.
Sequence Explorer can be used to extract nucleotide and protein sequences of particular genes, functional sites and other features. The sequences can be viewed by left-clicking features of interest in Sequence Explorer's map window and then copied by right-clicking the highlighted section of nucleotide/aminoacid sequence and choosing "Copy" button from the appearing submenu.
Currently, Sequence Explorer supports many editing operations, changing, creating and deleting features, etc. but does not have an option to save the edited data. Although such editing operations can be used to correct, modify and improve visual representation of annotated regions, the possibility to save changes / edited data should be implemented in future versions of the program.
The "Types of features" term is used to define the types of objects, such as operons, promoters, terminators, etc. that are located on a genomic sequence. The "Feature" term refers to a certain object of appropriate type that is located on a genomic sequence. For example, if we consider the CDS with ID 51 that is located in genome in positions from 178420 to 181153, then this certain CDS is referred to as "Feature", and the type of this "feature" is "CDS".