Alignment

From AAAWiki

Contents 1 Genome Alignments 1.1 Alignments of Freeze 1 Assemblies 1.2 Alignments of Older Assemblies 2 Gene Alignments 2.1 Alignments of Freeze 1 Assemblies 2.2 Externally available CAF1 Assembly Alignments 2.3 One-to-one ortholog CDS & peptide alignments

Genome Alignments

Alignments of Freeze 1 Assemblies

• MAVID/MERCATOR multiple whole genome alignments of 12 Drosophila genomes, including alignments restricted to internal branches of the tree (for instance, the melanogaster subgroup) (date: Nov. 1, 2006).
• PECAN/MERCATOR multiple whole genome alignments of 12 Drosophila genomes.
• MULTIZ multiple whole genome alignments of 12 Drosophila genomes and 3 other insects (mosquito, honeybee, red flour beetle).

MERCATOR bug report

Alignments of Older Assemblies

• MAUVE multiple whole genome alignments of 6 of the Drosophila genomes.
• MULTIZ multiple whole genome alignments between D. melanogaster and 6 other Drosophila genomes.
• VISTA genome browser, serving pairwise whole genome alignments between D. melanogaster and other sequenced genomes.

Gene Alignments

Alignments of Freeze 1 Assemblies

• GeneMapper multiple alignments of D. melanogaster FlyBase genes and their orthologs in the other 11 CAF1 genomes (README). The GeneMapper annotations on which the multiple alignments are based can be found here.

Externally available CAF1 Assembly Alignments

• David Garfield and Mohamed Noor (Duke Univ) have developed alignments for ~85% of the genes in the D. persimilis and D. pseudoobscura genomes. These alignments are based on the annotated CDS from the pseudoobscura genome project, and they may fill gaps in some of the many-species alignments available from UCSC and others. These alignments can be obtained at any time by contacting them.

One-to-one ortholog CDS & peptide alignments

• Amap-2.0, Kalign-2.01, MAFFT-5.861, Muscle-3.6 and Probcons-1.10 MFAs can be found in Ka/Ks_analyses:
  • CDS backtranslated from aa alignments.
  • Using venky models: dana.1-1_orthologs, dmel_longest_translation.FBgn, dpse.1-1_orthologs, dvir.1-1_orthologs, dere.1-1_orthologs, dmoj.1-1_orthologs, dsec.1-1_orthologs, dwil.1-1_orthologs, dgri.1-1_orthologs, dper.1-1_orthologs, dsim.1-1_orthologs, dyak.1-1_orthologs.

• Protein coding gene alignments can be found at FLYBASE.