developed by james estill, dept. of plant biology, university of georgia
DESCRIPTION
Developed by James Estill, Dept. of Plant Biology, University of Georgia. TriAnnot. France. IOB Cluster: UGA. Pipeline Annotate Wheat Sequences. PERL. GAME XML. BLAST –m 8 -d MIPS. BLAST –m 8 -d RB_pln. BLAST –m 8 -d TIGRGram. BLAST –m 8 -d TREP9nr. >HEX0014K09 GCAATACT CGGCACTT. - PowerPoint PPT PresentationTRANSCRIPT
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Developed by James Estill, Dept. of Plant Biology, University of Georgia
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Pipeline Annotate Wheat Sequences
PERL
TriAnnot
FranceIOB Cluster: UGA
GAME XML
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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
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Individual Program Procedure
Directoryof FASTAFiles
Configuration File
Run Program
RawResults
GFFFormated
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Developed by James Estill, Dept. of Plant Biology, University of Georgia
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!! 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.
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File requirements:1. Each fasta file contains a single record2. BAC scaffolds need to be merged to a single sequence3. Short header
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Repeat masking with RepeatMasker and TREP1. Softmask (using RepeatMasker)2. Convert softmask to hardmask because many gene prediction programs
are not softmasked aware
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Structural feature annotation: Includes currently only the annotation of gaps
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Gene annotation:1. Conduct gene prediction using TriAnnot pipeline2. Run individual gene prediction programs
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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
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NCBI-Blast: Most time-consuming step in the pipeline
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Transposable element annotation:1. By homology: RepeatMasker, NCBI-Blast2. By structural criteria: LTR-finder
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De Novo LTR Annotation Software
PubYear
Source
Availabili
OperatingS
ystem
Speed
Param
eterC
ontrol
License
TSD
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
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Preparing the computational results for Apollo1. Audit the computational results2. Concatenate the .gff files