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Figure 1 | BMC Bioinformatics

Figure 1

From: A universal genomic coordinate translator for comparative genomics

Figure 1

Overview of Kraken. (a) Showing Kraken’s input and output: genomes are supplied in FASTA format, synteny maps are in LASTZ general format, computed by any synteny based aligner such as LASTZ chained alignments [9], Satsuma [12], SyMAP [11], Enrodeo/Pecan alignment graphs [14]. Annotations are provided in Genome Transfer Format (GTF) files for one or more genomes, and can be either curated annotations, or experimentally found sequences, e.g. through Tophat/Cufflinks [18] or Trinity/PASA [19]. As output, Kraken lists the input GTF file items in output genome coordinates, as well as spatial relationships between translated features and features that are native to the genome. Features are hierarchically organized into loci, which are sets of transcripts, which are collections of exons. (b) Technical overview of Kraken’s workflow. Genomes and synteny maps are loaded, and a complete set of paths connecting each genome to each other is computed prior to processing. For each annotation, Kraken finds an exact or approximate orthology match in each other genome, and runs a two-step local alignment to determine the boundaries of the orthologous feature. Once completed, Kraken examines the locus-transcript-exon structure of the translated input and compares it, if available, to annotations native to the target genome.

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