Computational protocol: A universal genomic coordinate translator for comparative genomics

Similar protocols

Protocol publication

[…] Kraken reads the meta-data accompanying a dataset from a configuration file. This file lists the file locations of the genomes (FASTA format), the synteny maps (LASTZ general format and Satsuma format, Kraken provides conversion tools for other formats) and the genomes they connect and in what direction. Kraken requires the pre-computed pairwise synteny maps to provide the coordinates of orthologous regions (i.e. not the synteny alignments), in intervals specifying the corresponding: (i) chromosome or scaffold name; (ii) first nucleotide position in the interval; (iii) last nucleotide position in the interval. Maps need to be provided in one direction (genome A → genome B) only, and are duplicated and inverted in memory to supply both directions (genome B → genome A). All positions (start and stop) in the synteny maps are sorted by chromosome first and position next in target coordinates, setting up a data structure for binary search. [...] Detailed alignment of the source sequence is performed using the Cola [] implementation of a banded alignment with gap-affine penalties [,] against the target sub-sequence, which is defined by the offset determined by the rapid alignment. For source intervals of >100 nt, the sequence is split into two 100 nt chunks at each end covering the start and end region of the sequence, both in the source and the target genomes. A p-value threshold to accept alignments is configurable and defaults to 10−4. Alignments are not required to cover the entire source sequence, i.e. nucleotide mismatches at the boundaries are permissible (as forcing alignments would infer the risk of false insertions). In that case, the final translated target coordinates are estimated based on the alignment offset into the source sequence, i.e. if the alignment starts at position k in the source feature, the target start coordinate is adjusted by -k nucleotides (and vice versa for the final stop coordinate). Output is provided in GTF format, where for all the items that were successfully translated an output entry is produced containing the translated coordinates. […]

Pipeline specifications

Software tools LASTZ, Satsuma, Cola
Application Nucleotide sequence alignment
Organisms Mus musculus, Rattus norvegicus, Drosophila melanogaster, Homo sapiens, Pan troglodytes, Gorilla gorilla