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

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.

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

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

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

  3. BLAST –m 8-d MIPS BLAST –m 8-d RB_pln BLAST –m 8-d TIGRGram BLAST –m 8-d TREP9nr >HEX0014K09GCAATACTCGGCACTT Annotation Pipeline Gene Annotation TE Annotation Homology Homology De Novo De Novo GENSCANGENID FGENESH FindmiteLTR_StrucLTR_SeqFind_LTRLTR_Finder BLASTBLAT SIM4 HMMERRepeatmaskerTE NestBLAST

  4. Individual Program Procedure Configuration File Directoryof FASTA Files Run Program RawResults GFFFormated

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

  6. !! 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.

  7. File requirements: • Each fasta file contains a single record • BAC scaffolds need to be merged to a single sequence • Short header

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

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

  10. Gene annotation: • Conduct gene prediction using TriAnnot pipeline • Run individual gene prediction programs

  11. 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

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

  13. Transposable element annotation: • By homology: RepeatMasker, NCBI-Blast • By structural criteria: LTR-finder

  14. De Novo LTR Annotation Software Computation Annotation Good Neutral Bad Crap Best

  15. Preparing the computational results for Apollo • Audit the computational results • Concatenate the .gff files

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