Raw nuclear DNA Sequence
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<<comment>> Raw nuclear DNA Sequence SNAP EST2Genom e Chromosome I 690 curated gene models GeneWise RepeatMaske r EST2Genom e BLAT Ab initio gene detection <<comment>> Chromosome I 690 curated gene models <<comment>> 426,440 EST of apicomplexa EST Alignments Protein alignments TRF RepeatScout Repeat masking <<comment>> 1.2% of repeat sequences (75 kbp) <<comment> > Uniprot GAZE <<comment>> 5,419 gene models <<comment>> 44,545 EST have been aligned <<comment>> 1,426 gene models Figure S1
description
Raw nuclear DNA Sequence. RepeatMasker. 426,440 EST of apicomplexa. TRF. Repeat masking. Chromosome I 690 curated gene models. RepeatScout. 1.2% of repeat sequences (75 kbp). Uniprot. BLAT. Chromosome I 690 curated - PowerPoint PPT Presentation
Transcript of Raw nuclear DNA Sequence
<<comment>>Raw nuclear DNA Sequence
SNAP
EST2GenomeChromosome I 690 curated gene models
GeneWise
RepeatMasker
EST2Genome
BLAT
Ab in
itio
gene
de
tecti
on
<<comment>>Chromosome I690 curated gene models
<<comment>>426,440 EST of apicomplexa
EST
Alig
nmen
ts
Prot
ein
alig
nmen
ts
TRF
RepeatScout
Repe
at m
aski
ng
<<comment>>1.2% of repeat sequences (75 kbp)
<<comment>>Uniprot
GAZE
<<comment>>5,419 gene models
<<comment>>44,545 EST have been
aligned
<<comment>>1,426 gene models
Figure S1
<<comment>>Raw nuclear DNA Sequence
Snap detection EST/Prot mapping
GlimmerHMMGAZE
BlastX homology saturation
Delete CDS without homology overlapping CDS with homology
Create CDS presenting homology and delete overlapping CDS without homologies
Calculate start codon position by comparison with three best homologues
Delete in frame introns (mostly from GAZE)
Create intron to cover all ORFs in frames presenting BLASTX alignments from homologues
Split CDS with BLASTX alignment corresponding to different homologues
<<comment>>Similar to MegaBlast
<<comment>>Gene fusion event is
evaluated
Gene
stru
ctur
eGe
ne se
lecti
on
<<comment>>Homologues should have conserved ATG
position
Translate CDS in amino acids sequence
Best bidirectionnal hit and KEGG ID identification
<<comment>>Annotated DNA Sequence
3,513 gene models
Figu
re S
2Au
tom
atic
dete
ction
<<comment>>3,923 gene models
<<comment>>1,426 gene models
A.
B.
C.
D.
E.
Figure S3
A.
B.
Figure S4
0 500 1000 1300 Kbp
Chromosome I
Chromosome III
Chromosome II
Chromosome I
0 1000 2000 3000 Kbp
GAPD
H
CRM
P Tandem repeats Gap
Ia Ib
IIa IIb
IIIa IIIbIIIc
Ia Ib
FBA
CEN
CEN
REP
REP
N1-15
CEN
CEN
rDNA
N1-15
FBA
cDNA gDNA
RT- RT+
cDNA gDNA
RT- RT+
Bmldh Bmtpk
1000 bp -
Figure S5
Figure S6A
MDH-likeLDH of
apicomplexa
LDH-likeMDH
LDH
0.2
10095
100
100
100
100100
100
95
98
82
84
9210096
84100
100
A
88
Figure S6B
Eukaryota
Bacteria
Bartonella
100
90
88
97
10090
100
91
B
89
