Bioinformatics Leipzig

Publications - Supplemental material

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BIOINF 07-029: The Amphioxus Hox Cluster: Characterization, Comparative Genomics, and Evolution

Chris T. Amemiya, Sonja J. Prohaska, Alicia Hill-Force, April Cooke, Jessica Wasserscheid, David E. K. Ferrier, Juan Pacual Anaya, Jordi Garcia-Fernàndez, Ken Dewar, Peter F. Stadler

Sequences and Annotations

Primers

Amphioxus primer list. Formats: [csv] [pdf] [xls]

Amphioxus Hox Cluster Sequence Information

Amphioxus hox cluster sequence [fasta]
Amphioxus hox gene coding sequences [multi-fasta]
Amphioxus hox protein sequences [multi-fasta]
Partial AmphiHox9 cDNA and intron [pdf] [fasta]
In the PDF file the coding sequences are marked in yellow, the intron in blue

Amphioxus Hox Cluster Annotation Information

Amphioxus hox cluster annotation [text]
Homologies to Exon-1 sequences [blast-output]
Comparison of AmphiHox and Human HoxA and HoxD genes [pdf]
CDS is shown as blocks, introns as thin lines
Comparison of Amphioxus and Vertebrate IGR lengths [pdf]

Comparison with `brafl1` assembly

blastn comparision with brafl1 (Supplemental figure and caption) [pdf]

Polymorphisms

Protein polymorphisms [html-table]

Phylogenetic Footprinting

Hox Cluster Sequences Used for Comparison

hornshark	Heterodontus francisci	sequence [fasta]	HfM	HfB		HfD
		annotation [custom format]	HfM	HfB		HfD
coelacanth	Latimeria menadoensis	sequence [fasta]	LmA	LmB	LmC	LmD
		annotation [custom format]	LmA	LmB	LmC	LmD
frog	Xenopus tropicalis	sequence [fasta]	XtA	XtB	XtC	XtD
		annotation [custom format]	XtA	XtB	XtC	XtD
opossum	Monodelphis domestica	sequence [fasta]	MdA	MdB	MdC	MdD
		annotation [custom format]	MdA	MdB	MdC	MdD
mouse	Mus musculus	sequence [fasta]	MmA	MmB	MmC	MmD
		annotation [custom format]	MmA	MmB	MmC	MmD
dog	Canis familiaris	sequence [fasta]	CfA	CfB	CfC	CfD
		annotation [custom format]	CfA	CfB	CfC	CfD
human	Homo sapiens	sequence [fasta]	HsA	HsB	HsC	HsD
		annotation [custom format]	HsA	HsB	HsC	HsD

VISTA Plots

Hox 6-3 region [pdf]

`TRACKER` Analysis

Comparisons of the amphioxus Hox cluster with collections of orthologous vertebrate Hox clusters.

Set	Cluster	`tracker` ID	footprints

1	Bf+HoxA (HfM, LmA, MdA, MmA, CfA, HsA)	`02090346NVQD`	[text]
1	Bf+HoxB (HfB, LmB, MdB, MmB, CfB, HsB)	`02090402QWZB`	[text]
1	Bf+HoxC (LmC, MdC, MmC, CfC, HsC)	`02090422ORFT`	[text]
1	Bf+HoxD (HfD, LmD, MdD, MmD, CfD, HsD)	`02090501IBRQ`	[text]

2	Bf+Hf (HfM, HfB, HfD)	`02050243MJSO`	[text]
2	Bf+Lm (LmA, LmB, LmC, LmD)	`02030458OYKV`	[text]
2	Bf+Md (MdA, MdB, MdC, MdD)	`02050246JDNR`	[text]
2	Bf+Mm (MmA, MmB, MmC, MmD)	`02050250SBEK`	[text]
2	Bf+Cf (CfA, CfB, CfC, CfD)	`02050308GGXF`	[text]
2	Bf+Hs (HsA, HsB, HsC, HsD)	`02050303NFRO`	[text]

Footprint length distribution for set 1 [pdf]

RARE sites

RARE sites annotation file [custom format]