MapViewer Displays New Maps and
Annotation Tracks
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The Human Genome MapViewer has been enhanced with
new displays and color-schemes that show
additional data used by NCBI in annotating its latest build of the human
genome. Some existing maps have also been revised. Several of the principal
maps are described below.
The “Components” map shows the GenBank sequences that were used
to construct NCBI’s human genomic contigs, while the “GenBank”
map shows alignments of other human genomic sequences from GenBank that
were not used in the construction of the assembly. Gene Models predicted
within the assembly using GenomeScan show up on the “GenomeScan”
track. Dark brown models are those with BLAST hits to known vertebrate
proteins; the remainder of the GenomeScan models are drawn in light brown.
The Gene_Sequence map shows gene models that are color-coded by type of
supporting evidence. Blue models are based on mRNA alignments to the genomic
contigs with possible EST support, and are termed “Confirmed”
models. Green models are based only on EST alignments. Dark brown lines
indicate EST-supported GenomeScan models, while light brown lines indicate
GenomeScan models lacking EST support. Orange-colored lines flag models
in which a conflict exists between the model and an aligned mRNA.
When the Gene_Sequence map is made the master, two new links appear next
to the familiar links to the SequenceViewer (sv), the EvidenceViewer (ev),
and the Human/Mouse Homology Map (hm); these are the “seq” link
and the “mm” link. The “seq” link is used to download
the complete sequence for a gene model including a vari-able amount of
5' and 3' flanking sequence. The “mm” link invokes
the Model Maker, a new tool for the construction of model transcripts.
An article on the Model Maker appears on page 1 of this issue.
Transcript models produced by alignments of mRNA to the human genome are
shown on the “Transcript” map while the “UniGene_ Human”
and “UniGene_mouse” maps show the alignment of mRNA and EST
sequences from UniGene clusters to the human genome assembly. SAGE tag
mappings are shown on a new “SAGE_tag” track.
