Bioinformatics Research Laboratory

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Comparative Sequence Assembly

We used Pash to anchor WGS reads from the Rhesus macaque (Macaca mulatta) trace archive to the Hg16 build of the Human genome. Selected Human RefSeq genes and 20Kb flanking regions were used to drive our Comparative Sequence Assembly of the corresponding Rhesus sequence and scaffolding of the resulting contigs.

The data produced in our initial pipeline--including read anchorings to the Human genome, Rhesus contigs, scaffolded contigs, and 5-way MLAGAN alignments--are publicly available below.

Also available for these gene regions are our Pash anchorings of reads from the Chimp (Pan troglodytes) trace archive. These anchorings used the Hg15 draft of the Human genome.

See Footnotes

Download Comparative Assembly-Related Data

We provide several means of accessing the data:

Direct Access By RefGene Name or Accession Number
If we have assembly-related data for your RefGene, it will be shown and you can download what interests you.
Access Via Genboree
By entering a keyword, you will browse that area of the Human genome within the Comparative Assembly Genboree project. The data for an assembled region is available through the pop-ups for the "CSA:Mml.gene" track.
Download Data for an Entire Chromosome
We also provide tar-gzipped data sets by chromosome.

Comparative Assembly for Rhesus (version: May-10-2004)
Human Chromosome	M.ml WGS Read Anchorings	M.ml CSA Contigs	M.ml CSA Scaffolds	5-Species MLAGAN Alignments
Chr1	Read Anchorings	CSA Contigs	CSA Scaffolds	MLAGAN Alignments
Chr2	Read Anchorings	CSA Contigs	CSA Scaffolds	MLAGAN Alignments
Chr3	Read Anchorings	CSA Contigs	CSA Scaffolds	MLAGAN Alignments
Chr4	Read Anchorings	CSA Contigs	CSA Scaffolds	MLAGAN Alignments
Chr5	Read Anchorings	CSA Contigs	CSA Scaffolds	MLAGAN Alignments
Chr6	Read Anchorings	CSA Contigs	CSA Scaffolds	MLAGAN Alignments
Chr7	Read Anchorings	CSA Contigs	CSA Scaffolds	MLAGAN Alignments
Chr8	Read Anchorings	CSA Contigs	CSA Scaffolds	MLAGAN Alignments
Chr9	Read Anchorings	CSA Contigs	CSA Scaffolds	MLAGAN Alignments
Chr10	Read Anchorings	CSA Contigs	CSA Scaffolds	MLAGAN Alignments
Chr11	Read Anchorings	CSA Contigs	CSA Scaffolds	MLAGAN Alignments
Chr12	Read Anchorings	CSA Contigs	CSA Scaffolds	MLAGAN Alignments
Chr13	Read Anchorings	CSA Contigs	CSA Scaffolds	MLAGAN Alignments
Chr14	Read Anchorings	CSA Contigs	CSA Scaffolds	MLAGAN Alignments
Chr15	Read Anchorings	CSA Contigs	CSA Scaffolds	MLAGAN Alignments
Chr16	Read Anchorings	CSA Contigs	CSA Scaffolds	MLAGAN Alignments
Chr17	Read Anchorings	CSA Contigs	CSA Scaffolds	MLAGAN Alignments
Chr18	Read Anchorings	CSA Contigs	CSA Scaffolds	MLAGAN Alignments
Chr19	Read Anchorings	CSA Contigs	CSA Scaffolds	MLAGAN Alignments
Chr20	Read Anchorings	CSA Contigs	CSA Scaffolds	MLAGAN Alignments
Chr21	Read Anchorings	CSA Contigs	CSA Scaffolds	MLAGAN Alignments
Chr22	Read Anchorings	CSA Contigs	CSA Scaffolds	MLAGAN Alignments
ChrX	Read Anchorings	CSA Contigs	CSA Scaffolds	MLAGAN Alignments
ChrY	Read Anchorings	CSA Contigs	CSA Scaffolds	MLAGAN Alignments

FOOTNOTES

Data from the The Rhesus Genome Sequencing Project and the Chimpanzee Genome Sequencing Project were used for anchoring, comparative assembly, and MLAGAN comparison.

Please consult recent statements from NHGRI and the Wellcome Trust regarding the use restrictions on the unpublished sequences from genome projects.

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Bioinformatics Research Laboratory, HGSC
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( Modified Sep 07, 2008 )