1. Developed by James Estill, Dept. of Plant Biology, University of Georgia

2. Pipeline Annotate Wheat Sequences PERL TriAnnot France IOB Cluster: UGA GAME XML

3. Annotation Pipeline BLAST –m 8 -d MIPS BLAST –m 8 -d RB_pln BLAST –m 8 -d TIGRGram BLAST –m 8 -d TREP9nr >HEX0014K09 GCAATACT CGGCACTT Gene AnnotationTE Annotation De Novo Homology Findmite LTR_Struc LTR_Seq Find_LTR LTR_Finder HMMER Repeatmasker TE Nest BLAST De Novo Homology GENSCAN GENID FGENESH BLAST BLAT SIM4

4. Individual Program Procedure Directory of FASTA Files Configuration File Run Program Raw Results GFF Formated

10. Developed by James Estill, Dept. of Plant Biology, University of Georgia

13. !! 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.

14. File requirements: 1.Each fasta file contains a single record 2.BAC scaffolds need to be merged to a single sequence 3.Short header

15. Repeat masking with RepeatMasker and TREP 1.Softmask (using RepeatMasker) 2.Convert softmask to hardmask because many gene prediction programs are not softmasked aware

16. Structural feature annotation: Includes currently only the annotation of gaps

17. Gene annotation: 1.Conduct gene prediction using TriAnnot pipeline 2.Run individual gene prediction programs

18. GenMarkHMM: can be run locally (free license required) GENSCAN: Run on web server & convert output to.gff file FGeneSH: Run on web server & convert output to.gff file

19. NCBI-Blast: Most time-consuming step in the pipeline

21. Transposable element annotation: 1.By homology: RepeatMasker, NCBI-Blast 2.By structural criteria: LTR-finder

22. De Novo LTR Annotation Software Pub Year Source Availabili Operating System Speed Parameter Control License TSD LTR Dinucleotides PBS GAG IN RT RH PPT LTR_Struc 2003 LTR_Seq 2006 find_ltr 2007 LTR_Finder 2007 ComputationAnnotation Best GoodNeutralBadCrap

23. Preparing the computational results for Apollo 1.Audit the computational results 2.Concatenate the.gff files