Maize V4 TE Annotation Save

scripts and intermediate files used to annotate TEs in Jiao et al.

Project README


scripts and intermediate files used to annotate TEs in Jiao et al. 2016

LTR Retrotransposons

scripts in ltr

Software needed:

  • ncbi blast+

  • genometools, (download), need to pass 64bit=yes with-hmer=yes threads=yes to make, make install for ltrdigest hmm searches in parallel. I also had to pass cairo=no as well because I didn't have the right cairo libraries and it wouldn't compile otherwise

  • silix, (download), need to compile with --enable-mpi and --enable-verbose

  • hmmer (genometools with download and compile hmmer2 if you run make with-hmmer=yes)

Files needed, can be downloaded by in ltr directory:

  • download hmms of TE protein coding domains from gydb in directory gydb_hmms, will be used to identify protein coding domains of TE models

    -need to fix a hmm with name ty1/copia because this is used as a filename by ltrdigest. to remove the forward slash: sed -i "s#ty1/copia#ty1-copia#g" gydb_hmms/GyDB_collection/profiles/AP_ty1copia.hmm

  • download tRNAs of all eukaryotes


Scripts in sine/

Software needed:

  • SINE-Finder, download (This is a supplemental file at The Plant Cell; need to make executable, and rename to

    • I cannot make SINE-Finder function on reverse sequences. So I'm reporting SINEs only on the forward stand here, and will pick up sequences on the reverse strand with RepeatMasker.


Scripts in line/

Software needed:

TIR including MITEs

Scripts in tir/

Software needed:

  • detectMITE, download

  • TARGeT, download

  • mTEA, genometools (see above, already installed for ltr annotation)

    • mTEA needs fasta36 (specifically ggsearch36), bioperl, blast, muscle, supplied blogo directories to be put into PERL5LIB and PATH


Scripts in helitron/

Software needed:

Finding Homologous Fragments from Degraded TEs

Software needed:

Open Source Agenda is not affiliated with "Maize V4 TE Annotation" Project. README Source: mcstitzer/maize_v4_TE_annotation
Open Issues
Last Commit
5 years ago

Open Source Agenda Badge

Open Source Agenda Rating