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Genomes and
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chromosomes
Chromosomes, also called contigs or reference sequences, refer to one or more annotated sequences that form a genome assembly. For completed genome projects, these correspond to the sequence of a physical chromosome. Alternatively, it For less complete genomes, they 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.genomecontigs that correspond to parts of a physical chromosome.
Genome, genome version, or assembly: These terms refer to a group of chromosome sequences that you or another group assembled and made availableannotated sequences corresponding to the genome sequence of an organism. 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.
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Tracks
Tracks are rows of data that appear in the IGB interfaceread from the same file or data set. When you open a file, the data within the file will appear in one or more tracks. Older versions of IGB refered referred to tracks as "tiers" and so you may see this term used elsewhere in the User's guide.
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. There are three main types of tracks: Graph tracks, Annotation tracks, and Reference Sequence tracks. Alignment tracks and Probe Set tracks are types of Annotation Track.
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Annotation tracks
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.
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- single-coordinate feature: splice sitessite
- single-span feature, with strand: an exon
- single-span feature, no strand: sequence recognized by a restriction siteenzyme
- multi-span feature, with strand: a gene model
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Graphs tracks
Graphs consists of are numeric data associated with regions or single-base positions in a chromosome.
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Sequence track
Sequences are sets of DNA residues comprising a chromosomefrom a chromosomes or contigs that together make an assembly. Sequences can be fully or partially loaded from local files, QuickLoad Quickload sites, or DAS servers. IGB allows you to examine sequence data in a separate window called Distributed Annotation Servers. You can view sequence data in the Coordinates track or by opening the Sequence Viewer.
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Alignments
Alignments represent how sequences obtained from an experiment (such as sequence reads from an RNA-Seq experiment) align onto the a 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, insertions, or deletions. At higher zoom, the aligned sequence bases become visible. File formats for alignments include BAM and PSLX.
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Probe set alignments
Probe set alignments consists consist of a Affymetrix probe set target sequence sequences aligned onto a chromosome and the location of probes relative to the aligned target sequence. This data type is Affymetrix-specific.the reference with probe locations indicated as annotations on the target sequence alignments. The probes are kind of annotation on an annotation.
These data are Affymetrix specific.
