Evolutionary Analysis of the Protein Domain Distribution in Eukaryotes

Dissertation of Arli Aditya Parikesit

Supplementary materials of the Dissertation:

  1. AUGUSTUS Gene Predictors (AUG Format). The content of the compressed file is the AUGUSTUS annotations in AUG format. Each individual annotation file has the information of the species name and the assembly. The content of each annotation file is the gene, transcript, exon, intron, and CDS coordinates. The provinsional transcript and gene ids are given as well. The protein sequences and strand are integrated as part of the AUG format [tar.gz]

  2. AUGUSTUS Gene Predictors (FASTA Format) . The content of the compressed file is the protein of AUGUSTUS annotations in FASTA format. Each individual annotation file has the information of the species name and the assembly. [tar.gz]

  3. SUPERFAMILY and PFAM Domain Annotations (.list format) . The content of the compressed file is the SUPERFAMILY and PFAM domain annotations. Each individual annotation file has the information of the species name and the domain annotation database [ SUPERFAMILY (sf) or PFAM (pfam)]. The content of each annotation file is the gene id, e-value, domain coordinate, domain-id, and domain description [tar.gz]

  4. Transcription Factor Domain Mapping . The SUPERFAMILY domains list of the Transcription Factor. The content of the file is the domain-id, fold type, and domain description [.list]

Correspondence regarding the dissertation should be addressed to Arli Aditya Parikesit at arli(at)bioinf.uni-leipzig.de

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