prof e r t ep assembly annotation tools for repeats
TRANSCRIPT
ASSEMBLYANNOTATION TOOLS FOR REPEATS
Nina Hoštáková May 2018
PROFR
EP
DANTE
REPEAT EXPLORER
PROFREP DANTE
NGSreads
automatic clusters
classification clusters
domains DB
domains classification
RE archive
PROFREP DANTE
Domains GFFRepeats GFFN GFF Profiles BigWig
Domains sequences
Repeats distributionQuantitative info Annotation Tracks Phylogenetic
relations
Domain-based ANnotation Of Transposable ElementsPROFiles of REPeats
PROFREP
Domains GFFRepeats GFFN GFFProfiles BigWig
DNA
ProfRep RefinerProfRep MaskerGFF Region Selector
RE ARCHIVE
Data Preparation
Prepared Datasets
ORPisumSativumTerno (2015)
NGSreads
automatic clusters
classification clusters
Extract Datafor ProfRep
ProfRepReducingcd-hit
Representativereads
Reducedclusters
RE ARCHIVE
Data preparation -PROFREP-
42 repeat|mobile_element|Class_I|LTR|Ty1/copia|SIRE48 repeat|satellite|PisTR/B134 organelle|plastid
>1fCGTAATATACATACTTGCTAGCTAGTTGGATGCATCCAACTTGCAAGCTAGTTTGATG>1rGATTTGACGGACACACTAACTAGCTAGTTGCATCTAAGCGGGCACACTAACTAACTAT
>CL42 2 1624460f 63975r >CL48 1 882044r
bp
hits
CL1 None/unclassified
DNA seq
97f
487f
34f
2854r
150f
Ty1/copia|Angela
Principle -PROFREP-
CL3
chromovirus|Tekay
28f
ALL
2f
70r
3141f
250f
1502r 1741f
22r
8r
277f
bp
hits
Ty1/copia|Angelachromovirus|Tekay
> Threshold hits
> Threshold bp
1 10000
AvePID = 90 %
Principle -PROFREP-
1. PROFILES
2. GFF3
1 6000
AvePID = 90 %
All
DOMAINS [DANTE]
REPEATS [ProfRep]
Athila
Ogre/Tat
CACTA
satellite
GENES [Ensembl]
Theobroma cacao assembly (2014), chr 9 Distributions
DOMAINS [DANTE]
REPEATS [ProfRep]
REFINED REPEATS [ProfRep]
REPEATS ANNOTATION [Ensembl]
PROFILE [ProfRep]
Theobroma cacao assembly (2014), chr 9 Chromovirus|Tekay element
N [ProfRep]
DANTEDomains Finder
DNA
DANTEDomains Filter
TE Domains DBDomains Classification
Primary Domains GFF
Filtered Domains GFF
Translated Domains Seqs
Viridiplantae
(Metazoa)
● ELEMENT TYPE
● DOMAIN TYPE
● QUALITY ➔ Identity ➔ Similarity ➔ Relative length ➔ Interruptions
Relaxed conditions
Stringent conditions
DNA
DomainsDatabase hits
Cluster
Principle -DANTE-
DNA x PROT similarity search
+ - +
DNA
database hits
score threshold
best hit
Hits classifications
RT|Class_I|LTR|Ty3/gypsy|non-chromovirus|OTA|Ogre/Tat|TatVRT|Class_I|LTR|Ty3/gypsy|non-chromovirus|OTA|Ogre/Tat|TatVRT|Class_I|LTR|Ty3/gypsy|non-chromovirus|OTA|Ogre/Tat|TatVRT|Class_I|LTR|Ty3/gypsy|non-chromovirus|OTA|Ogre/Tat|TatIV/OgreRT|Class_I|LTR|Ty3/gypsy|non-chromovirus|OTA|Ogre/Tat|TatIV/Ogre
Common classification level
RT Class_I|LTR|Ty3/gypsy|non-chromovirus|OTA|Ogre/Tat
8756 9241
Principle -DANTE-
OTA|Ogre/Tat
Visualization -DANTE-
Class_I|LTR|Ty3/gypsy|non-chromovirus|OTA|Ogre/Tat|TatV
New element
REPEATS ANNOTATION [Banana Genome Hub]
DOMAINS[DANTE]
Musa acuminta assembly (2016), chr 1 Ogre/Tat| TatV element