developed by james estill, dept. of plant biology, university of georgia
TRANSCRIPT
Developed by James Estill, Dept. of Plant Biology, University of Georgia
Pipeline Annotate Wheat Sequences
PERL
TriAnnot
FranceIOB Cluster: UGA
GAME XML
Annotation PipelineBLAST –m 8-d MIPSBLAST –m 8
-d RB_plnBLAST –m 8-d TIGRGramBLAST –m 8
-d TREP9nr>HEX0014K09GCAATACTCGGCACTT
Gene Annotation TE Annotation
De Novo HomologyFindmiteLTR_StrucLTR_SeqFind_LTRLTR_Finder
HMMERRepeatmaskerTE NestBLAST
De Novo HomologyGENSCANGENIDFGENESH
BLASTBLATSIM4
Individual Program Procedure
Directoryof FASTAFiles
Configuration File
Run Program
RawResults
GFFFormated
Developed by James Estill, Dept. of Plant Biology, University of Georgia
!! THIS DOCUMENT IS UNDER CURRENT DEVELOPMENT!!
This program manual and the scripts that make up the DAWG-PAWS package are under current development. Everything is subject to change without notice at this point. This software comes as is, without any expressed or implied warranty. Use at your own risk.
File requirements:1. Each fasta file contains a single record2. BAC scaffolds need to be merged to a single sequence3. Short header
Repeat masking with RepeatMasker and TREP1. Softmask (using RepeatMasker)2. Convert softmask to hardmask because many gene prediction programs
are not softmasked aware
Structural feature annotation: Includes currently only the annotation of gaps
Gene annotation:1. Conduct gene prediction using TriAnnot pipeline2. Run individual gene prediction programs
GenMarkHMM: can be run locally (free license required)GENSCAN: Run on web server & convert output to .gff fileFGeneSH: Run on web server & convert output to .gff file
NCBI-Blast: Most time-consuming step in the pipeline
Transposable element annotation:1. By homology: RepeatMasker, NCBI-Blast2. By structural criteria: LTR-finder
De Novo LTR Annotation Software
Pub
Year
Source
Availabili
OperatingS
ystem
Speed
Param
eterC
ontrol
License
TS
D
LTR
Dinucleotides
PB
S
GA
G IN
RT
RH
PP
T
LTR_Struc 2003
LTR_Seq 2006
find_ltr 2007
LTR_Finder 2007
Computation Annotation
Best Good Neutral Bad Crap
Preparing the computational results for Apollo1. Audit the computational results2. Concatenate the .gff files