Prediction of contiguous regions in the amniote ancestral genome

This page contains additional material for the paper "Prediction of contiguous regions in the amniote ancestral genome", to appear in the proceedings of ISBRA 2009.

Input data

Species tree (picture).
Genomic markers
- PECAN alignments (without platypus and with only alignments that are located on well defined chromosomes).
- Coordinates.
- Human genome coverage by genomic markers (red segments represent genomic markers) and position of markers.
- Chicken coverage by genomic markers (red segments represent genomic markers) and position of markers.
Gene families.

Whole genome alignments used to compute genomic markers were downloaded from ftp.ensembl.org:/pub/release-50/emf/ensembl-compara/pecan_12_amniota. Orthologous genes from the considered species were downloaded from the Ensembl (release 51) Compara homology database using data Biomart. Gene families were computed using transitive orthologies, and discarding unassigned genes, genes assigned to random chromosomes, non-X sex chromosomes or mitochondrial genome.

Results

We first give the data for the ancestral genome described in section 3.1 of the paper.

Set of all ancestral syntenies. Each line represents a synteny with the following format: label|weight:list of genomic markers.
Set of discarded ancestral syntenies.
Double Conserved Syntenies. Each line that is not commented (symbol #) represents a DCS between an amniote genome and a teleost genome.
PQ-tree from the above conserved syntenies: PQ tree. Symbol _Q (resp. Q_, _P, P_) indicates the beginning of a Q node (resp. end of a Q node, beginning of a P node, end of a P node). (PQR tree before optimization).
Coverage by colinear segments of the human genome and chicken genome.
Chromosomal associations. Each line of the below files represents a CAR and the list of chromosomes of an extant species (human or chicken) that contains genomic markers of this CAR.
- Chicken genome.
- Human genome.
Adjacencies and support:
- General support of all adjacencies.
- Support by ancestral syntenies (maximal common intervals) obtained by comparing two ingroups (chicken vs. mammalian): ingroups
- Support by ancestral mammalian syntenies included into DCS DCS_mammalian.
- Support by DCS: DCS.

Results obtained with other values of min_prop: