1 Feature Rendering
This section covers features that use generic feature rendering settings. The features (SNPs, structural variants, clone placements, and segmental duplications) that require special handling are covered in the later sections. 1.1 Feature Color Code
Feature type
Color Visual Examples
Gene Green
RNA Blue
Coding region Red
All other features
Black
1.2 Special Rendering Styles
For features with special attributes, special rendering will be applied.
1.2.1 Genes marked as pseudo Settings Visual Effect Visual Examples
All features are
shown in one gene
group Stripes over green gene bar
Gene bar is hidden Green stripe background  Gene bar and gene
label are hidden
Green stripe background
1.2.2 Features with exception text Exception Example
Visual Effect Visual Examples
Mismatch in transcription Shaded background  Mismatch for
translation Shaded background
Unclassified
transcription discrepancy
Shaded background
1.2.3 Feature location marked as partial Example Visual Effect Visual Examples
Partial start
Black “<<” or “>>”
at 5’ end
Partial stop
Black “<<” or “>>”at 3’ end
Partial start and stop
Black “<<” and “>>” at both ends
1.2.4 Features marked as partial Example Cases Visual Effect
Visual Examples
Example includes a partial feature (marked as white “<<” and “>>”) and features with partial stop (marked as black “>>”)
White “<<” and “>>” at both ends
1.3 Feature Decorations
Different feature decoration styles are solely for offering different ways of visualization.  The exact same feature can be rendered using each of the five existing styles.
Décor Styles Visual Effect
Visual Examples
Default
Solid bars for feature intervals or exons, and solid lines for introns
Arrows
Arrows at both ends showing the strand, and lighten bars for introns
Square anchor
Square for feature start, arrow for feature stop, dash lines for introns
Circle anchor
Circle for feature start, arrow for feature stop, dash lines for introns
Fancy
Circle for mRNA start only, square for other features start except for gene and CDS, arrow for feature s
top, lighten bars for mRNA introns, and canted lines for CDS
introns
Note: the glyphs representing feature start and stop will be rendered only when their sizes can fit into the first and last intervals.
2Gene Model Features
A Gene Model is a feature group that contains four main features: gene, mRNA, CDS and
Exon.  The group may also contain SNP and other features that are projected from mRNA and CDS products.
2.1 Gene Model Rendering
Rendering Options Visual Examples
Show all
Show all transcripts and CDSs,
no gene bar
Merge transcript and CDS pairs,
no gene bar
Merge all transcripts and CDSs,
no gene bar
Show on single line with exon
structure
Gene bar only
With SNP features projected
from mRNA and CDS products
With other features projected
from mRNA and CDS products
2.2 Special Rendering for CDS Features
When zoomed into the sequence level, both annotated protein sequence and translated protein sequence are shown for CDS features.
2.3 Feature Ruler
For a selected RNA or CDS feature, a feature ruler will be show with the feature’s local
coordinate.
3Clone Placement Features
3.1 Clone Display
types是什么意思Display Description
Unique, concordant,
Real ends
Multiple,
concordant, Real
ends
Unique not Set,
Concordant, Real
ends
Unique, discordant,
Real ends
Multiple, discordant,
Real ends
Unique not set,
discordant, Real
ends
Unique, Concordant not set, Real ends
Multiple, Concordant not set, Real ends
Unique not set, Concordant not set, Real ends
Unique, Concordant, One virtual end
Multiple, Concordant, One virtual end
Unique not set, Concordant, One virtual end
Unique, Discordant, One virtual end
Multiple, Discordant, One virtual end
Unique not set, Discordant, One virtual end
Unique, Concordant not set, One virtual end
Multiple, Concordant not set, One virtual end
Unique not set, Concordant not set, One virtual end
Clone with no end, no strand
Clone with no end, plus strand
Clone with no end, no strand, multiple, concordant not set
Clone with no end, plus strand, discordant, unique not set

版权声明：本站内容均来自互联网，仅供演示用，请勿用于商业和其他非法用途。如果侵犯了您的权益请与我们联系QQ:729038198，我们将在24小时内删除。