1 Feature Rendering
This ction covers features that u generic feature rendering ttings. The features (SNPs, structural variants, clone placements, and gmental duplications) that require special handling are covered in the later ctions. 1.1 Feature Color Codecircle是什么意思
Feature type
Color Visual Examples
Gene Green
RNA Blue
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Coding region Red财务负责人岗位职责
wide
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 pudo Settings Visual Effect Visual Examples
11月的英文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
you know
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 Cas Visual Effect
a m
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 featur
e stop, lighten bars for mRNA introns, and canted lines for CDS
introns
Note: the glyphs reprenting 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 quence level, both annotated protein quence and translated protein quence are shown for CDS features.
2.3 Feature Ruler
For a lected RNA or CDS feature, a feature ruler will be show with the feature’s local
coordinate.
3Clone Placement Features
3.1 Clone Display
Display Description
threedaysUnique, concordant,
Real ends
Multiple,
concordant, Real
ends
Unique not Set,
Concordant, Real
ends
Unique, discordant,
Real ends
Multiple, discordant,
Real ends
Unique not t,
discordant, Real
ends
Unique, Concordant not t, Real ends
Multiple, Concordant not t, Real ends
Unique not t, Concordant not t, Real ends
Unique, Concordant, One virtual end
Multiple, Concordant, One virtual end小学英语教学论文网
Unique not t, Concordant, One virtual end
Unique, Discordant, One virtual end
Multiple, Discordant, One virtual end
例如用英语怎么说
Unique not t, Discordant, One virtual end
Unique, Concordant not t, One virtual end
Multiple, Concordant not t, One virtual end
Unique not t, Concordant not t, One virtual end
Clone with no end, no strand
Clone with no end, plus strand
Clone with no end, no strand, multiple, concordant not t
Clone with no end, plus strand, discordant, unique not t
