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rdowell's bookmarks matching tag Alignment
 
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Combining statistical alignment and phylogenetic footprinting to detect regulatory elements
Combining Statistical Alignment and Phylogenetic Footprinting to Detect Regulatory Elements
R Satija, L Pachter, and J Hein
Bioinformatics (Oxford, England) 24 (10), btn104v1 (18 Mar 2008)
info:pmid/18353788 | info:doi/10.1093/bioinformatics/btn104
Posted by rdowell and 5 others with 1 comment to Alignment on Wed May 07 2008 at 13:52 UTC | info | related
 
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
J D Thompson, D G Higgins, and T J Gibson
Nucleic acids research. 22 (22), 4673-80 (11 Nov 1994)
info:pmid/7984417
Posted by rdowell and 9 others to clustalw tool Alignment on Tue Dec 04 2007 at 19:18 UTC | info | related
 
Fast and sensitive multiple alignment of large genomic sequences.
Michael Brudno et al.
BMC bioinformatics [electronic resource]. 4 (1), 66 (23 Dec 2003)
info:pmid/14693042 | info:doi/10.1186/1471-2105-4-66
Posted by rdowell and 2 others to Alignment tool on Tue Dec 04 2007 at 19:16 UTC | info | related
 
LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA.
Michael Brudno et al.
Genome Research 13 (4), 721-31 (01 Apr 2003)
info:pmid/12654723 | info:doi/10.1101/gr.926603
Posted by rdowell and 3 others to LAGAN Alignment tool on Tue Dec 04 2007 at 18:48 UTC | info | related
 
MAVID: constrained ancestral alignment of multiple sequences.
Nicolas Bray and Lior Pachter
Genome research 14 (4), 693-9 (Apr 2004)
info:pmid/15060012 | info:doi/10.1101/gr.1960404
Posted by rdowell and 1 other to mavid tool Alignment on Fri Nov 09 2007 at 18:17 UTC | info | related
 
AVID: A global alignment program.
Nick Bray, Inna Dubchak, and Lior Pachter
Genome research 13 (1), 97-102 (Jan 2003)
info:pmid/12529311 | info:doi/10.1101/gr.789803
Posted by rdowell to avid tool Alignment on Fri Nov 09 2007 at 18:17 UTC | info | related
 
Fast algorithms for large-scale genome alignment and comparison.
Arthur Delcher et al.
Nucleic acids research 30 (11), 2478-83 (01 Jun 2002)
info:pmid/12034836
Posted by rdowell to MUMmer tool Alignment on Fri Nov 09 2007 at 18:14 UTC | info | related
 
Aligning multiple genomic sequences with the threaded blockset aligner.
Mathieu Blanchette et al.
Genome research 14 (4), 708-15 (Apr 2004)
info:pmid/15060014 | info:doi/10.1101/gr.1933104
Posted by rdowell and 5 others to multiz tool Alignment on Fri Nov 09 2007 at 18:09 UTC | info | related
 
BLAT---The BLAST-Like Alignment Tool
BLATthe BLASTlike alignment tool
W Kent
Genome Research, GR-2292R (20 Mar 2002)
info:doi/10.1101/gr.229202.%20Article%20published%20online%20before%20March%202002
Posted by rdowell and 2 others to tool Alignment yeast on Fri Nov 09 2007 at 18:06 UTC | info | related
 
Human-mouse alignments with BLASTZ.
Scott Schwartz et al.
Genome research 13 (1), 103-7 (Jan 2003)
info:pmid/12529312 | info:doi/10.1101/gr.809403
Posted by rdowell and 3 others to blastz tool Alignment on Fri Nov 09 2007 at 18:06 UTC | info | related

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