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[Drosophila] EvoPrinterHD is now available

Thomas Brody via dros%40net.bio.net (by brodyt from ninds.nih.gov)
Thu Sep 20 08:13:37 EST 2007


A new comparative genomics sequence analysis tool has just been made
available to the public. EvoPrinterHD creates automated alignments of
sequences of all 12 Drosophila genomes or selected subsets.
 
The site can be accessed at the following URL:
http://evoprinter.ninds.nih.gov/

Full instructions are available at
http://evoprinter.ninds.nih.gov/aboutevopHD.htm

Below is a list of innovations incorporated into EvoPrinterHD.

EvoPrinter Upgrades:
 
1. In addition to twelve Drosophila genomes, five nematode and twenty
vertebrate genomes have been included in the automated alignments.
2. A repeat finder program has been added to identify single and multi-copy
repeat sequences within your input DNA.
3. Enhanced-BLAT (eBLAT) alignment (3 superimposed pair-wise alignments
generated with different search and alignment parameters) identifies up to
75% more conserved sequences between evolutionarily distant orthologs than
the original BLAT alignment.
4. Intra-genomic aligning region search programs identify rearrangement(s)
and/or duplication(s) that contain conserved sequences.
5. Composite eBLATs allow for the visual detection of rearranged and/or
duplicated conserved sequences within the different species aligning
regions.
6. A color-coded EvoDifferences profile identifies unique differences that
each species contributes to the final EvoPrint.
7. A composite eBLAT option allows for the inclusion of rearranged sequences
within a single EvoPrint readout.
8. Parsing and curation of selected conserved sequences for the comparative
analysis of different conserved sequence blocks. The conserved sequence
curator option allows for the automatic extraction and annotation (name and
numbering) of selected conserved sequences in both forward and reverse
complemented orientations.
9. To minimize alignment times, EvoPrinterHD currently employs twin 2.8
GHz/64GB RAM dual quad-core processors that operate in parallel to
simultaneously query multiple genomes. Twenty kb input DNA alignments to 5
nematode or 12 fly genomes average under 10 seconds and for 20 vertebrate
genomes, a 20 kb input DNA alignment takes ~25 seconds.


The original EvoPrinter is described in the following paper:

Odenwald WF, Rasband W, Kuzin A, Brody T. (2005).
EVOPRINTER, a multigenomic comparative tool for rapid identification of
functionally important DNA. Proc Natl Acad Sci 102(41): 14700-5

Please contact me with any questions or comments at brodyt from ninds.nih.gov

Tom Brody




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