Genomes and Chromosomes
chromosome: In IGB, chromosome refers to any single sequence. Typically this corresponds to the sequence of a physical chromosome. Alternatively, it may represent an assembled contig corresponding to part of a physical chromsome. All chromosomes in IGB are assumed to be DNA, rather than RNA sequences. No two chromosomes within the same genome version can have the same name.
genome, genome version, assembly: These terms refer to a group of chromosome sequences that you or another group assembled and made available. IGB designates these using the month and year they were published or made publicly available. For example, NCBI versions 35 and 36 of the human genome are considered to be two separate genome assemblies. Each one contains multiple chromosome sequences, including the expected chromosomes 1 to 22, X and Y. Other sequences, such as "chr22_random" are also considered distinct chromosomes for the purposes of display in IGB.
Every sequence in IGB is identified by its genome version and chromosome names, which must therefore be distinct.
Tracks
Tracks are rows of data that appear in the IGB interface. When you open a file, the data within the file will appear in one or more tracks. Older versions of IGB refered to tracks as "tiers" and so you may see this term used elsewhere in the User's guide.
Annotations
Annotations indicate the known or suspected locations of genomic features such as genes, exons, promoter regions, pseudogenes, and so forth. Annotations may consist of a single coordinate, a single span with a start and end positions, or a collection of spans. Most annotations reside on either the plus or minus strand of a chromosome, but some do not.
Examples of annotations include:
- single-coordinate feature: splice sites
- single-span feature, with strand: an exon
- single-span feature, no strand: a restriction site
- multi-span feature, with strand: a gene model
Graphs
Graphs consists of numeric data associated with regions or single-base positions in a chromosome.
Sequences
Sequences are sets of DNA residues comprising a chromosome. Sequences can be fully or partially loaded from local files, QuickLoad sites, or DAS servers. IGB allows you to examine sequence data in a separate window called the Sequence Viewer.
Alignments
Alignments represent how sequences obtained from an experiment (such as reads from an RNA-Seq experiment) align onto the reference genomic sequence. At low zoom they look like annotations, but with marks representing mismatches between the read and the reference genome whenever these data are available. At higher zoom, the aligned sequence bases become visible. File formats for alignments include BAM and PSLX.
Probe set alignments
Probe set alignments consists of a target sequence aligned onto a chromosome and the location of probes relative to the aligned target sequence. This data type is Affymetrix-specific.